Length–weight relationships of fish species in the freshwater rift valley lakes of Kenya

This study reports length–weight relationships for 10 species of fish encountered in the only two freshwater lakes wholly in the Rift Valley of Kenya, Naivasha and Baringo. In Lake Naivasha, none of the species analysed was native to the lake. Two were introduced species non‐native to East Africa (Micropterus salmoides, Cyprinus carpio), with three native to East Africa but not to the lake (Tilapia zillii, Oreochromis leucostictus, Barbus paludinosus). In Lake Baringo, all species were native (Oreochromis niloctictus baringoensis, Labeo cylindricus, Barbus intermedius autralis, Barbus lineomaculatus, Clarias gariepinus). Specimens were collected by gill netting in September 2004 and October 2005. With the exception of B. lineomaculatus, the b values in the relationship W = aL^b were between 2.90 and 3.22.     

Fish condition in introduced tilapias of Ugandan crater lakes in relation to deforestation and fishing pressure

This study identifies environmental predictors of the condition of two introduced tilapia species (Oreochromis leucostictus and Tilapia zillii) that are known to have divergent trophic niches (planktivore and herbivore, respectively) in 17 crater lakes in western Uganda. We asked whether fish condition differs among lakes characterized by differences in fishing pressure and catchment deforestation; and we related relative condition factor to gradients of environmental variation across lakes. Lakes characterized by severe catchment deforestation tended to be lakes with high fishing pressure, so it was difficult to explore independent and interactive effects. However, mean relative condition factor was higher in populations with high fishing pressure compared to populations with low fishing pressure for both O. leucostictus and T. zillii. The condition of O. leucostictus populations was higher in lakes with severely deforested catchments; but mean relative condition factor of T. zillii did not differ between deforestation categories. Principal components analysis (PCA) was used to describe the major environmental gradients of variation among the lakes; and PCA factor scores were regressed against relative fish condition. The association between fish condition and environmental gradients was stronger for O. leucostictus than for T. zillii. For O. leucostictus, fish condition was related to PC1 (43% of the variance) and factors that loaded most heavily included Chl-a, water transparency, lake area and depth, suggesting higher condition in lakes characterized by higher primary productivity and smaller size. For T. zillii, PC3 (11%) was the only axis related to fish condition; and factors that loaded most heavily included lake area (positive), and conductivity and total nitrogen (negative). Some of the larger lakes are characterized by higher availability of macrophytes that may positively affect the food base for T. zillii.     

Changes in fish species composition in Lake Naivasha,Kenya

The fish species composition in Lake Naivasha has been modified during recent years. Out of seven introduced and one indigenous species reported in 1962, only three introduced ones are found today. The elimination of species has been brought about by predation and changing ecological conditions. The most common fish species today is Sarotherodon leucosticuus. The hybridization found by previous workers between S. leucostictus x S. spilurus niger has stopped, as S. s. niger is no longer found in the lake. Most of the hybrid characters have been lost by the few surviving hybrids due to backcrossing between hybrids and between hybrids and S. leucostictus. The hybrids now mostly resemble S. leucostictus.     

The introduced <Emphasis Type="Italic">Micropterus salmoides</Emphasis> in an equatorial lake: a paradoxical loser in an invasion meltdown scenario?

Micropterus salmoides is a North American piscivorous fish on the IUCN list of 100 of the world’s worst invasive alien species. Introduced into Lake Naivasha (Kenya) in 1929, their current population abundance is significantly depressed in a lake that has recently become dominated by fishes of the Cyprinidae family; the introduced cyprinid Cyprinus carpio now dominates catches in the commercial fishery and Barbus paludinous is now numerically dominant in the fish community. Long-term diet studies of M. salmoides based on gut contents analysis (GCA) have defined their diet spectrum, feeding preferences and ontogenetic dietary shifts. Between 1987 and 1991, diet was size-structured; fish <260 mm were mainly insectivorous and fish >260 mm fed mainly on invasive crayfish Procambarus clarkia with B. paludinosus rarely taken. More recent GCA data revealed that up to 2003, these size-structured trophic relationships were still evident, but there has been a subsequent shift to their feeding almost exclusively on small (<100 mm) B. paludinosus, coincident with a size-related functional switch whereby M. salmoides >120 mm were now piscivorous. However, a Bayesian stable isotope mixing model (SIAR) suggested M. salmoides diet actually remained relatively varied in 2006 and 2007; it indicated P. clarkii were still contributing more to their diet than B. paludinosus in fish <260 mm and provided only partial support for the functional shift. The consequence of the M. salmoides depressed population abundance is their predation pressure on prey fishes is limited and preventing top-down effects. This is in contrast to their invasive populations elsewhere in the world and the likely result of invasion meltdown processes in Naivasha involving the introduced C. carpio and P. clarkii that have produced sub-optimal foraging conditions for M. salmoides.     

The smell of danger: chemical recognition of fish predators by the invasive crayfish Procambarus clarkii

1. Since avoiding predation can compromise animal fitness, prey are expected to respond to different predator species with an intensity appropriate to the level of risk. In fresh waters, the threat of predation is typically assessed by chemical cues, in particular by odours released by either injured/disturbed conspecifics (conspecific alarm odour) or predators (predator odours). Here, we used the most widely distributed crayfish in the world, the invasive North American Procambarus clarkii, to investigate the relative effectiveness of odours emitted by fish predators compared with conspecific alarm odour. We also tested whether P. clarkii is able to discriminate between fish predators of which it has ‘experience’ (either recent, via introduction to the same water body, or old, by sharing a native range), as well as between fish predators that pose low or high risk. 2. The study was carried out on introduced populations of P. clarkii from two sites, characterised by different fish assemblages: the Malewa River (a tributary of Lake Naivasha, Kenya) and Lake Trasimeno (Italy). Laboratory experiments consisted of three sequential phases (‘water’, ‘food’ and ‘smell’ phases) and five treatments. Treatments differed in the odour presented during the smell phase, i.e. no odour (plain water) and odours from either injured conspecifics or three fish species per site. Crayfish from the Malewa River population were confronted with the odours of largemouth bass (Micropterus salmoides), common carp (Cyprinus carpio) and tilapia (Tilapia zillii) (all introduced to Lake Naivasha but absent from the Malewa River), and those from the Lake Trasimeno population with the odours of the introduced largemouth bass and carp and the native chub (Squalius cephalus). Largemouth bass is the only predator that imposes a high risk to crayfish, and it also shares its native range with P. clarkii. We analysed the time spent by crayfish feeding, in locomotion and in adopting a raised or lowered posture. A reduction in the time spent feeding and in locomotion, and an increase in the time spent in the lowered posture were considered to indicate alarm. 3. Crayfish from both populations responded with a more pronounced reduction in feeding to conspecific alarm odour rather than to predator odours. Crayfish from the Malewa River reacted with the same intensity to the odours of the three fish species tested, whereas, in Lake Trasimeno, the odour of largemouth bass was significantly more threatening than the odours of the other two species. 4. Procambarus clarkii seems to perceive a general fish odour that alerts it to possible predation risk without the need of either a direct recent experience or via sharing a common native range. However, where they coexist with fish, crayfish become able to distinguish among species, adapting the intensity of their response to the effective risk. Our results confirm the relatively high learning capacity of P. clarkii reported in previous studies and suggest the existence of mechanisms that make predator recognition particularly efficient in this extraordinarily successful invader.     

The role of alien fish (the centrarchid Micropterus salmoides) in lake food webs highlighted by stable isotope analysis

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Climate Change Expands the Spatial Extent and Duration of Preferred Thermal Habitat for Lake Superior Fishes

Climate change is expected to alter species distributions and habitat suitability across the globe. Understanding these shifting distributions is critical for adaptive resource management. The role of temperature in fish habitat and energetics is well established and can be used to evaluate climate change effects on habitat distributions and food web interactions. Lake Superior water temperatures are rising rapidly in response to climate change and this is likely influencing species distributions and interactions. We use a three-dimensional hydrodynamic model that captures temperature changes in Lake Superior over the last 3 decades to investigate shifts in habitat size and duration of preferred temperatures for four different fishes. We evaluated habitat changes in two native lake trout (Salvelinus namaycush) ecotypes, siscowet and lean lake trout, Chinook salmon (Oncorhynchus tshawytscha), and walleye (Sander vitreus). Between 1979 and 2006, days with available preferred thermal habitat increased at a mean rate of 6, 7, and 5 days per decade for lean lake trout, Chinook salmon, and walleye, respectively. Siscowet lake trout lost 3 days per decade. Consequently, preferred habitat spatial extents increased at a rate of 579, 495 and 419 km² per year for the lean lake trout, Chinook salmon, and walleye while siscowet lost 161 km² per year during the modeled period. Habitat increases could lead to increased growth and production for three of the four fishes. Consequently, greater habitat overlap may intensify interguild competition and food web interactions. Loss of cold-water habitat for siscowet, having the coldest thermal preference, could forecast potential changes from continued warming. Additionally, continued warming may render more suitable conditions for some invasive species.     

Nearshore fish habitat utilization and species associations in Lake Opinicon (Ontario,Canada)

Synopsis The bulk of Lake Opinicon fish biomass is concentrated in the physically diverse inshore areas. Quantitative analysis of the community compositions of the various inshore habitat types (weedy inlets, sandy shallows, rock shelf, gravel, etc.) showed that each supported a characteristic assemblage of fishes with a relatively constant species and year class composition. This was maintained throughout the season despite a drop in fish biomass in late summer when there was a progressive movement into the offshore waters.Weedbed areas supported the highest biomass, and greatest species and year class diversity. Thereafter, in declining order of richness, were rocky and sandy areas. A few fish species were restricted to single habitat types, e.g.Notropis heterodon to inshore weedbeds.Lepomis macrochirus, the commonest species in the lake was, by contrast, versatile and occurred in all inshore habitats. Commonly the numbers of a species in a habitat differed between day and night. Significant diel movements between habitats characterized two nocturnal feedersPomoxis nigromaculatus andIctalurus nebulosus.     

Deciphering lifelong thermal niche using otolith δ18O thermometry within supplemented lake trout (Salvelinus namaycush) populations

1. The selection of thermal habitat by fish is strongly regulated by physiology and behaviour. However, delineation of a species lifelong thermal niche remains technically challenging. Lake trout (Salvelinus namaycush) survival and productivity are recognised as being tightly linked to a somewhat restricted thermal habitat. The factors guiding temperature selection during each life stage remain poorly understood.
2. In this study, we tested the significant factors controlling the realised thermal niche of lake trout from two southern Quebec small boreal lakes that experienced supplementation stocking during the last 20 years. We used oxygen stable isotope (δ¹⁸O) thermometry of otolith calcium carbonates (aragonite) using secondary-ion mass spectrometry to estimate experienced lifelong temperatures. We investigated the thermal habitat of lake trout with known genotypes (local, hybrid, and stocked).
3. Ontogeny and genetic origin influenced temperature selection in both studied lake trout populations. Young-of-the-year consistently used warmer, shallower habitats (10.7 ± 2.6°C, 7.5 m depth) prior to a juvenile transition to colder and deeper waters (8.5 ± 3.3°C, 10 m depth). Stocked lake trout, originating from a genetically distinct ecotype, exhibited a more variable thermal niche, with some individuals consistently using warmer habitat (10.4 ± 1°C) than local fish. Their hybrid progeny also occupied a warmer thermal niche, intermediate to the parental strains. We propose that increased fat content and genetic origin are potential explanatory factors for warmer temperature use.
4. This study reiterates that high-resolution otolith δ¹⁸O thermometry is a uniquely well-suited approach for unravelling the multiple factors that influence lifelong temperature selection in fish. Our results illustrate that the realised thermal niche is influenced by a genetic–environment interaction.

     

Effects of flow on lateral interactions of fish and shrimps with off-channel habitats in a large river-floodplain system

Off-channel habitats play a crucial role in the life-cycles of many riverine fish species, but lateral movements of fish into these habitats are poorly understood. We tested how flow dynamics affects the movement of fish and shrimps between the main river channel and different types of off-channel habitats: a riverine lake and a wetland. Our study site was the lower Waikato River, North Island, New Zealand, where there are numerous off-channel habitats. Fish were sampled using directional fyke nets. Shortfin eel (Anguilla australis) migrated mostly into the wetland at night, particularly during high river flows. Common bullies (Gobiomorphus cotidianus) were most abundant during the day and in low-discharge conditions, moving mostly into the riverine lake, whereas freshwater shrimp (Paratya curvirostris) moved mostly into the wetland. High numbers of non-native larval common carp (Cyprinus carpio) moved out of the wetland with retreating flood water. This study emphasises the importance of lateral connectivity and flooding in functioning of this river system where numerous native fish, but also exotic fish, used off-channel habitats. Floodplain management strategies should promote ‘controlled connectivity’ measures that provide access for native species at key times while limiting opportunities for introduced species to utilise their favoured off-channel habitats.     

Trophic Niche Segregation in the Nilotic Ichthyofauna of Lake Albert (Uganda, Africa)

Synopsis Nile perch, Lates niloticus, and Nile tilapia, Oreochromis niloticus, were originally transplanted from Lake Albert in western Uganda to the African Great Lakes, Lake Victoria and Lake Kyoga, where they are partially implicated in reduction of the fish species diversity. Lake Albert is facing multiple environmental changes, including declining fish species diversity, hyper-eutrophication, hypoxia, and reduced fish catches. To examine the role of Nile perch and Nile tilapia in the food web in their native Lake Albert, we estimated their diets using stable nitrogen and carbon isotopes. In Lake Albert, the tilapiine congeners (closely related species), Tilapia zillii, Oreochromis leucostictus, and Sarethorodon galilaeus, and the centropomid Nile perch congener, Lates macrophthalmus, have narrower diet breath in the presence of the native O. niloticus and L. niloticus. A computerized parameter search of dietary items for five commercially important fish species (Hydrocynus forskahlii, Bagrus bayad, L. niloticus, Alestes baremose and Brycinus nurse) was completed using a static isotopic mixing model. The outcome of the simulation for most fish species compared favorably to previously published stomach contents data for the Lake Albert fishes dating back to 1928, demonstrating agreement between stable isotope values and analyses of stomach contents. While there were some indications of changes in the diets of L. niloticus and A. baremose diets over the past 20 years in parallel with other changes in the lake, for the most part, food web structure in this lake remained stable since 1928. The Lake Albert fish assemblage provides insight into the invasion success of L. niloticus and O. niloticus.     

Aspects of the ecology of the prickly sculpin,Cottus asper Richardson,a persistent native species in Clear Lake,Lake County,California

Synopsis The biology of the prickly sculpin was investigated in Clear Lake, Lake County, California in order to determine how it has persisted in the face of introductions of numerous exotic species when most other native species have declined in abundance or have become extinct. Sculpins over 15 mm SL inhabited all types of benthic habitats in the lake, while post larval sculpins were pelagic when the postlarvae of exotic species were absent. The feeding ecology of sculpins was distinct from the other fishes in the lake in that they fed largely on amphipods and chironomid midge larvae regardless of the time of year, time of day, or habitat. Sculpins were uncommon in the stomachs of piscivorous fishes, except juvenile largemouth bass (Micropterus salmoides). It is concluded that prickly sculpins have persisted in Clear Lake in part because they are ecologically distinct from the exotic species and are not preyed upon by them to any great extent, and in part because they have managed to survive other man-related perturbations of this ecosystem.     

The rise of potentially toxin producing cyanobacteria in Lake Naivasha,Great African Rift Valley,Kenya

Lake Naivasha, an important inland water ecosystem and a crucial freshwater resource in the Great African Rift Valley, has displayed clear signals of degradation in recent decades. We studied the phytoplankton composition and biomass levels in the period 2001–2013 and noted a progressive increase in the occurrence of potentially toxic cyanobacteria. Analyses for the presence of cyanotoxins such as microcystins (MC), cylindrospermopsin (CYN) and anatoxin-a (ATX-a) were carried out on samples collected in 2008–2013. Among the cyanotoxins tested, low concentrations of MC were detected in the lake. This is the first record of the occurrence of MC in Lake Naivasha. For the first time, molecular phylogenetic investigations of field clones of cyanobacteria from Lake Naivasha were carried out to establish the taxa of the dominant species. Amplification of the aminotrasferase (AMT) domain responsible for cyanotoxin production confirmed the presence of the mcyE gene belonging to the microcystin synthesis gene cluster in field samples containing Microcystis and Planktothrix species. These findings suggest that toxin producing cyanobacteria could become a threat to users of this over-exploited tropical lake in the near future.     

The Spatial Pattern of the Small Fish Community in the Biandantang Lake – A Small Shallow Lake Along the Middle Reach of the Yangtze River, China

The spatial pattern of the small fish community was studied seasonally in 1996 in the Biandantang Lake. Based on plant cover, the lake was divided into five habitats, arranged in the order by plant structure complexity from complex to simple: Vallisneria spiralis habitat (V habitat), Vallisneria spiralis–Myriophyllum spicatum habitat (V–M habitat), Myriophyllum spicatum habitat (M habitat), Nelunbo nucefera habitat (N habitat), and no vegetation habitat (NV habitat). A modified popnet was used for quantitative sampling of small fishes. A total of 16 fish species were collected; Hypseleotris swinhonis, Ctenogobius giurinus, Pseudorasbora parva, Carassius auratus and Paracheilognathus imberis were the five numerically dominant species. In both summer and autumn, the total density of small fishes was about 10indm^–2. Generally, Ctenogobius giurinus, a sedatory, benthic fish, was distributed more or less evenly among the five habitats, while the other four species had lower densities in the N habitat and NV habitat, which had the simplest structures. The distribution of the small fish species showed seasonal variations. In winter, most species concentrated in the V habitat, which had the most complex structure. In spring, the fish had low densities in the N and NV habitat, and were more or less evenly distributed in the other habitats. In summer, the fish had a low density in the NV habitat, and were evenly distributed in the other habitats. In autumn, the fish had higher densities in the V–M and M habitats than in the others. Generally, spatial overlaps between the dominant species were higher in winter than in the other seasons. It was suggested that the variations in the importance of predation risk and resource competition in habitat choice determined the seasonal changes of spatial patterns in the small fishes in the Biandantang Lake.     

Two hundred years of a diverse Daphnia community in Lake Naivasha (Kenya): effects of natural and human-induced environmental changes

1. We used fossil diapausing eggs extracted from ²¹⁰Pb‐dated sediment cores to reconstruct historical changes in the Daphnia community of Lake Naivasha, a climate‐sensitive lake in Kenya which over the past 200 years has experienced a series of well‐documented natural and anthropogenic environmental changes. 2. Contiguous sampling and analysis of four cores yielded ephippial capsules of eight Daphnia species. Only two of these had been recorded previously in live collections from Lake Naivasha, and one species is new to science. The four more common species (Daphnia barbata, D. laevis, D. magna, and D. pulex) show striking differences in abundance patterns and population dynamics through time. Four other species (D. lumholtzi, D. curvirostris, D. longispina s.l., and Daphnia sp. nov. type Limuru.) appear to have been present only occasionally. Nevertheless, between 1895 and 1915 seven species of Daphnia inhabited Lake Naivasha simultaneously. 3. Despite considerable natural environmental change associated with climate‐driven lake‐level fluctuations, the Daphnia community of Lake Naivasha has been severely affected by human activities over the past century, especially the introduction of exotic fishes and water‐quality changes because of agricultural soil erosion. The recent reappearance of large‐bodied Daphnia species (D. magna, D. barbata, D. lumholtzi, Daphnia sp. nov. type Limuru) after 20–110 years of absence can be explained by their release from fish predation, following a dramatic increase in turbidity caused by excess clastic sediment input from eroded catchment soils. The small‐bodied species D. laevis has fared less well recently, presumably because the benefit of lowered predation pressure is counteracted by more pronounced negative effects of increased turbidity on this species and loss of submerged macrophyte beds which formerly served as predation refuge. 4. Our results suggest that, despite considerable environmental instability and the absence of specialised zooplanktivores, top‐down control of fish on large zooplankton is important in Lake Naivasha. Predation pressure from fish has led to clear‐cut shifts in local Daphnia species composition, but failed to drive the larger taxa to extinction.     

Population structure and secondary productivity of Limnodrilus hoffmeisteri (Claparede) and Branchiura sowerbyi Beddard in the profundal zone of Lake Naivasha,Kenya

Lake Naivasha has been well studied since the 1930s but attempts to understand its ecological functioning have had to wait until enough was known about its structure. The energetics of the lake has only been studied to date at primary producer level. Following the identification of the invertebrate components of the littoral and profundal benthos, this study was initiated. The absence of native fish species in Lake Naivasha, combined with a fishery based only on three, introduced species, added an applied dimension to the work. The introduction of additional fish species which will utilize unexploited ecological niches has been suggested. The benthic invertebrates form one such niche. Two oligochaetes dominated the community, Branchiura sowerbyi Beddard and Limnodrilus hoffmeisteri Claparade. The former had a productivity of 7.4 g m^–2 ann^–1 (as dry weight), the latter 0.6. These figures are not particularly high and do not support the introduction of a new fish species on their own.     

Population changes in sympatric Great and Long-tailed Cormorants (Phalacrocorax carbo and P. africanus): the effects of niche overlap or environmental change?

Between January 1993 and January 1995, the number of Great Cormorants (Phalacrocorax carbo) using Lake Naivasha, Kenya (00° 45 S, 36° 20 E) for foraging and resting increased 56%, while the number of sympatric Long-tailed Cormorants (Phalacrocorax africanus) decreased 64%. In 1995 and 1996, we documented habitat changes and conducted monthly population and resource-use surveys of the two species in an attempt to discover the most likely reasons for these changes. The increase in Great Cormorants was probably the result of immigration from nearby Lake Nakuru due to extreme water level reductions there. Lake Naivasha also experienced falling water levels and transparency during this period, but these changes were not as severe and are not considered likely reasons for the decline in Long-tailed Cormorant numbers. Despite some probable dietary overlap, the two species were well separated in terms of foraging locations, foraging methods, resting habitats and breeding timing. The decline in Long-tailed Cormorant numbers may be connected with increased disturbance by fishermen along the lake littoral, this species' primary feeding location.     

Shrimps of an ancient Balkan lake: Bionomy and conservation

In order to have a comprehensive evaluation and classification of the natural biota of Lake Pamvotis, the present study aims at investigating shrimps’ bionomic traits. Information on shrimps’ habitat preferences, abundances, and syntopic species in relation to the physicochemical profile of the lake’s water are investigated for the first time. The study was carried out on a bi-monthly base, at six littoral sites of the lake. Samples’ study from different habitats and seasons revealed that the freshwater shrimp Atyaephyra thyamisensis was the most abundant species, accounting for 44.76% of the total taxa catch, while the grass shrimp Palaemonetes antennarius was less abundant (7.54%). Syntopic fish species in the littoral zone of Lake Pamvotis such as Economidichthys pygmaeus, Gambusia holbrooki, Knipowitschia caucasica and Rutillus panosi showed interannual differences with abundances of 24.12%, 19.13%, 4.26% and 0.20%, respectively. Correspondence analysis revealed clear patterns between species and stations. A. thyamisensis was predominant in shallow, well oxygenated water bodies rich with aquatic vegetation, but it was absent from deeper habitats. P. antennarius was found mainly in lentic water bodies, rocky substratum and deeper habitats. Taking into account the high ecological importance of the freshwater shrimps in ecosystems’ energy flow, ecological and biological data of lake’s shrimps are discussed and presented thoroughly. Threats and conservation measures for both shrimp species are debated also in detail.     

Shifts in the food of Nile tilapia, Oreochromis niloticus (L.) in Lake Victoria, Kenya

Studies of the food of introduced Nile tilapia, Oreochromis niloticus (L.) with respect to size, habitat and season were conducted between November 1998 and October 2000 in Kenyan waters of Lake Victoria. Stomach contents of 1980 specimens collected by demersal trawl and seining were analysed. Nile tilapia originally known to be herbivorous, feeding mostly on algae has diversified its diet to include insects, fish, algae and plant materials. The major diet of fish <5 cm total length was zooplankton whereas bigger fish included a wider range of food items in their diet. There was spatial variation in diet with insects and algae dominating in the gulf and open water habitats respectively. There was no seasonal variation in the food items ingested and diel feeding regime indicated that O. niloticus is a diurnal feeder. The shift in diet could be due to ecological and environmental changes in Lake Victoria, which have been associated with changes in composition and diversity of fish and invertebrate fauna, emergence and dominance of different flora including water hyacinth Eichhornia crassipes (Mart.) Solms‐Laub., and algae communities. The feeding habit of O. niloticus is discussed in the context of changes occurring in the lake.     

Habitat Use by Fishes in Coral Reefs,Seagrass Beds and Mangrove Habitats in the Philippines

Understanding the interconnectivity of organisms among different habitats is a key requirement for generating effective management plans in coastal ecosystems, particularly when determining component habitat structures in marine protected areas. To elucidate the patterns of habitat use by fishes among coral, seagrass, and mangrove habitats, and between natural and transplanted mangroves, visual censuses were conducted semiannually at two sites in the Philippines during September and March 2010–2012. In total, 265 species and 15,930 individuals were recorded. Species richness and abundance of fishes were significantly higher in coral reefs (234 species, 12,306 individuals) than in seagrass (38 species, 1,198 individuals) and mangrove (47 species, 2,426 individuals) habitats. Similarity tests revealed a highly significant difference among the three habitats. Fishes exhibited two different strategies for habitat use, inhabiting either a single (85.6% of recorded species) or several habitats (14.4%). Some fish that utilized multiple habitats, such as Lutjanus monostigma and Parupeneus barberinus, showed possible ontogenetic habitat shifts from mangroves and/or seagrass habitats to coral reefs. Moreover, over 20% of commercial fish species used multiple habitats, highlighting the importance of including different habitat types within marine protected areas to achieve efficient and effective resource management. Neither species richness nor abundance of fishes significantly differed between natural and transplanted mangroves. In addition, 14 fish species were recorded in a 20-year-old transplanted mangrove area, and over 90% of these species used multiple habitats, further demonstrating the key role of transplanted mangroves as a reef fish habitat in this region.