Prawn community structure in the subtropical Mfolozi–Msunduzi estuarine system,KwaZulu-Natal,South Africa

The life cycles of many marine and freshwater prawn species are closely associated with estuarine habitat. Here, the prawn community of the Mfolozi–Msunduzi estuarine system is described and the system's potential as an alternative nursery for prawns during prolonged closure of the adjacent St Lucia estuarine system is examined. Sampling was conducted at five localities in summer and winter in 2007–2012. The Mfolozi–Msunduzi Estuary is a river-dominated system with mouth condition, sediment grain size and turbidity being the most important factors affecting the structure of its prawn community. Twelve prawn species were recorded, including five marine penaeid and five freshwater palaemonid species. The prawn community was numerically dominated by freshwater Macrobrachium equidens and two penaeids, Fenneropenaeus indicus and Metapenaeus monoceros. Significant differences were recorded between summer and winter samples, with freshwater species dominating the catch in summer, while penaeid species were dominant in winter. The marked seasonal change in the prawn community was related to strong river flows during summer creating low-salinity conditions, unsuitable for penaeid postlarval development, throughout most of the system. Compared to St Lucia, the Mfolozi–Msunduzi Estuary can be regarded as a poor alternative nursery area for penaeids during the summer peak postlarval recruitment period.     

Mesozooplankton community structure changes in the Mfolozi–Msunduzi estuarine system,South Africa,during contrasting river flow conditions

The Mfolozi–Msunduzi estuarine system is subject to periodic dry and wet cycles, with subsequent changes in the abiotic and biotic characteristics of the system. The aim of the current study was to compare its mesozooplankton composition during relatively dry and wet periods. Mesozooplankton samples were collected between 2007 and 2010 in both the Mfolozi and the Msunduzi, covering a dry period between 2007 and 2008 and a period of relatively high freshwater inputs during 2009 and 2010. High flows during the wet period reduced the densities of most of the dominant estuarine mesozooplankton taxa in the Mfolozi Estuary, such as estuarine calanoids Pseudodiaptomus stuhlmanni (Poppe & Mrázek, 1895) and Acartiella natalensis (Connell & Grindley, 1974). The Msunduzi Estuary functioned as a reservoir from which recolonisation by estuarine taxa would quickly take place after the Mfolozi was scoured by floodwaters. Densities of dominant meroplankton taxa, such as zoeae of the crab Paratylodiplax blephariskios and Macrobrachium spp., were not noticeably different in the Mfolozi–Msunduzi system between the low- and high-flow periods.     

Tidal behaviour of post-larval penaeid prawns (Crustacea: Decapoda: Penaeidae) in a southeast African estuary

Although the post-larvae of many species of inshore penaeid prawns migrate from the sea into estuarine habitats the mechanisms by which this process occurs have not been adequately explained. Collections of penaeid post-larvae in the St. Lucia estuary in Natal, South Africa during flood and ebb tides, day and night, were dominated by Penaeus japonicus Bate and P. indicus Milne Edwards. P. indicus was most abundant over flood tides, day and night but P. japonicus was markedly more nocturnal and only abundant over night floods. Vertical distribution differed in the two species. P. japonicus was more abundant in bottom samples but this was much less apparent in P. indicus. It is suggested that movement into the water column is triggered by pressure changes and this is modified by light, salinity, and the nature of the substratum. These responses are discussed in relation to the invasion of estuaries by penaeid post-larvae and the apparent survival of P. indicus but not P. japonicus in the St. Lucia system.     

Chwaka Bay (Zanzibar,East Africa) as a nursery ground for penaeid prawns

The penaeid prawns are recruited in the sheltered sandy beaches and mangrove areas of Chwaka Bay (Zanzibar) at post-larval stage (7 mm). Year round incursions with a maximum during the warmer months of December to March were observed. February to March is considered as the peak recruitment period. Out of six species of penaeids represented in the area, Penaeus latisulcatus (75%) and Penaeus indicus (15%) were dominant. The recruitment pattern indicated greatest incursions of post-larvae with the flood spring tides of the night when the tidal flow is strong.The juvenile population of P. latisulcatus is distributed in those intertidal sandflats with a rich growth of seagrass and P. indicus in the muddy areas of mangrove forests. P. indicus showed affinity for euryhaline conditions, whereas P. latisulcatus showed no preference for lower salinity. Provision of food and shelter are considered as important factors for their nursery dependence. P. latisulcatus attained a size of 60–70 mm in five to six months and P. indicus 110–120 mm in six to eight months during their nursery phase. These juvenile penaeids were found to be omnivorous, feeding on animal products, plant material and detritus.The maturing P. latisulcatus emigrate back to the sea when they are about 65 mm, whereas P. indicus move out at about 120 mm. A positive correlation between post-larval recruitment and juvenile abundance was observed.     

Fish communities in temporarily open/closed estuaries from the warm- and cool-temperate regions of South Africa: A review

The majority of estuaries along the coastline of southern Africa are termed temporarily open/closed estuaries (TOCEs) and are closed off from the sea for varying periods by a sandbar which forms at the mouth. It is therefore important to understand the processes occurring within TOCEs and their importance to fishes in order to make sound management recommendations. Estuaries along the coast of South Africa and their associated fish assemblages are biogeographically distinct and occur in either a subtropical, warm-temperate or cool-temperate zone. There are 125 TOCEs found within the cool-temperate and warm-temperate zones. Most fish species found in TOCEs are the juveniles of marine taxa that breed at sea. Permanently open estuaries generally have a higher diversity of species than TOCEs, but TOCEs still provide important nursery areas for many marine species and numerically often have a higher proportion of estuarine resident species. Important taxa in terms of abundance and biomass in warm-temperate TOCEs include the sparids Rhabdosargus holubi and Lithognathus lithognathus, several mugilid species, estuarine residents (particularly Gilchristella aestuaria and Atherina breviceps) and the freshwater cichlid Oreochromis mossambicus. The diversity of fishes in cool-temperate TOCEs is low when compared with warm-temperate systems and Liza richardsonii tends to dominate catches by number and mass in most systems. Several species recorded in TOCEs show clear longitudinal distribution trends. For example Atherina breviceps is generally more abundant in the lower reaches of estuaries. Mouth state, particularly the frequency, timing and duration of mouth opening plays a key role in determining species richness, composition, diversity and abundance in TOCEs. Mouth state is directly linked to freshwater input. Reduced river inflow leads to prolonged mouth closure and shorter open phases, which inhibits immigration and emigration of marine fish species between estuaries and the sea. Understanding of the effects of various processes occurring within these systems, particularly variation in freshwater input, on the biota of these important systems facilitates the development of informed management recommendations.     

Spatial distribution and seasonality of ichthyoplankton and anthropogenic debris in a river delta in the Caribbean Sea

Temporal changes in larval fish species composition and abundance compared with other components of the seston are described in four estuarine habitats in the Atrato Delta, Colombia. In comparison with zooplankton, fish larvae and egg density and anthropogenic debris abundance were low in the South Atrato Delta. Transparency, water temperature and chlorophyll a were the major factors influencing the spatiotemporal distribution of ichthyoplankton in the delta. The most abundant fish larvae were Astyanax sp. 1, Anchovia clupeoides, Cetengraulis edentulus, Anchoa sp., Bathygbius curacao, Dormitator maculatus, Hyporhamphus sp., Atherinella blackburni, Gobiosoma sp. 1 and Menticirrhus americanus (92·8% of total abundance). Spatial temporal analysis shows that in this delta, shrub (arracachal) and grass (eneal) habitats are important for freshwater and estuarine species, whilst mudflat and mangrove are important for estuarine species and estuarine–marine species, since most flexion and post‐flexion stages of these species were found there. Anthropogenic debris density never surpassed the total ichthyoplankton density, but was ubiquitous. Shrub and mangrove habitats had higher densities of anthropogenic debris, since these are flood‐stem habitats that trap solids.     

Does the flatfish community of the Mondego estuary (Portugal) reflect environmental changes?

Temporal and spatial patterns of abundance of the flatfish community in the Mondego estuary were investigated from 2003 to 2007, based on monthly beam trawl samples. During the study period there was a severe drought, with consequential reductions in river runoff. A total of eight flatfish species occurred within the estuary, with seasonal specific richness and abundance varying considerably. It was possible to identify three main groups: one composed of species present throughout the study period and in high densities: Platichthys flesus and Solea solea (maximum densities 3.7 and 4.1 Ind 1000 m^?2, respectively); a second group of less abundant but regularly present species: Scophthalmus rhombus and Solea senegalensis (maximum densities 0.2 and 0.3 Ind 1000 m^?2, respectively); and a third group of occasional species that occurred only during the drought period: Arnoglossus laterna, Buglossidium luteum, Dicologlossa hexophthalma and Pegusa lascaris. Flatfish distribution patterns varied according to the estuarine use guild: marine‐estuarine dependent fish occurred mainly in the upper reaches, while marine stragglers and marine‐estuarine opportunists occurred mostly in the downstream areas. Species with more northern latitudinal affinities were the most affected by the drought, related with a lesser extent of river plumes to the coastal area, resulting in a reduction in half of the abundance levels. However, flatfish species with more southern affinities increased in abundance during the drought, benefiting also from an increase in estuarine water temperature. Early summer salinity and precipitation values were good proxies for estimating abundance levels of P. flesus and S. solea, respectively, emphasizing the importance of hydrodynamics for the recruitment and abundance of these commercially important species.     

A REVIEW OF THE MACROBENTHIC FAUNA OF THE MHLATHUZE ESTUARY: SETTING THE ECOLOGICAL RESERVE

Summary

This paper reviews historical and current ecological information on macrobenthos from the Mhlathuze Estuary before and after development of the Richards Bay Harbour. The fauna is described in terms of the potential influence of a change in freshwater inflow to the system and the requirements for the setting of an Ecological Reserve. Over 95% of the species recorded were primarily marine and to a lesser extent estuarine in origin. Fauna typical of sheltered, soft-bottomed marine environments inhabited the estuary, whereas estuarine fauna was limited to the canalised sections of the Mhlathuze River. Certain areas were characterised by opportunistic species indicative of disturbed or organically enriched sediments while others sustained a high diversity of more sensitive climax species, several of which are endemic to southern Africa. The majority of species belonged to the Class Polychaeta but the estuarine mudcrab Paratylodiplax blephariskios dominated the benthic biomass. The pre-feasibility stage of the Ecological Reserve Determination indicated that a reduction in freshwater input would negatively impact upon the already reduced estuarine component at the head of the estuary. Conversely, if freshwater flow to the estuary is augmented, sediment transport via the river could increase without there being an. improved catchment management policy in place.     

Distribution patterns of the fish assemblage in the Mamanguape River Estuary,North-eastern Brazil

The Mamanguape River Estuary was studied along a continuum ranging from shallow sandstone reefs adjacent to the river mouth up to the limit of influence of seawater, the upper portions of the estuary. Fish samples were gathered using three types of nets along 17 sample sites, grouped in four regions according to salinity range (reefs and low, middle and upper estuaries), to seasonality (dry and rainy seasons) and to habitat usage (marine visitor, marine estuarine-opportunist, marine estuarine-dependent, estuarine resident and estuarine &; marine). Differences were found in the fish assemblages along the estuarine-reef gradient, with most species (n?=?30) being considered marine, estuarine-opportunists or estuarine-dependent, according to its abundance and distribution. A low number of species (n?=?11) were considered estuarine residents. Some species exhibited significant differences in spatial distribution pattern, in which juveniles and adults predominated in different portions of the estuary, suggesting an ontogenetic migration both in relation to the adjacent reef area and across estuarine regions. Several species were newly recorded in the Mamanguape Estuary: Anchoa spinifer, Halichoeres poeyi, Hyporhamphus roberti, Scomberomorus cavalla, Sphyraena barracuda and Ocgocephalus vesperilio.     

The composition and community structure of the ichthyofauna of the upper Scheldt estuary: synthesis of a 10-year data collection (1991–2001)

Fish collections on the cooling water filter screens of the Doel power plant were used to analyse temporal trends in estuarine fish populations of the upper Scheldt estuary, Belgium. Between 1991 and 2001, 62 species shared the estuary, with 15 species present at any one time. Identified were 23 marine stragglers, 16 freshwater species and four diadromous species, but their contribution to the total catch was insignificant. In terms of numbers, marine estuarine opportunists (17 species) mainly occurring as juveniles and estuarine residents (two species) were the dominant life cycle categories. Six fish species contributed to >97% of the total catch: three Pomatoschistus species [P. minutus (32%), P. microps (30%) and P. lozanoi (6%)], two Clupeidae [Clupea harengus (16%) and Sprattus sprattus (8%)] and Syngnathus rostellatus (5%). Abundance of almost all species in the estuary was highly seasonal and characterized by pronounced abundance peaks. Ordination of the data showed that variability in the temporal structure of estuarine fish community was first determined by differences in annual recruitment and then by predictable, cyclical patterns of species abundance.     

Mesozooplankton of the Kosi Bay lakes,South Africa

The Kosi coastal lake system, a chain of four interconnected basins, is located in the subtropical north-eastern corner of South Africa. Little information is available on zooplankton of the system and the main aim of this study is to report on zooplankton samples collected during 2002 and 2003. The set of samples consists of seasonal, subsurface mesozooplankton samples that were collected during nighttime in each of the lakes. A well-developed salinity gradient was evident along the interconnected lakes in the subsurface water during all seasons, ranging from freshwater in the upper lake Amanzamnyama to a maximum of 22 recorded in Lake Makhawulani. The zooplankton community structures of the lakes reflected the salinity gradient of the system, with some coastal marine taxa recorded in the lakes closer to the mouth and only freshwater taxa recorded in Lake Amanzamnyama. Mesozooplankton diversity and abundance were relatively low compared to other estuarine systems along the eastern coast of South Africa. The dominant taxa were calanoid copepods Acartiella natalensis and Pseudodiaptomus stuhlmanni and the mysid Mesopodopsis africana in the lower lakes, whereas cyclopoids Mesocyclops sp. and Thermocyclops sp. dominated the freshwater lake Amanzamnyama.     

Recruitment and growth of two small‐bodied resident fish species (Gobiidae and Atherinidae) in oligohaline,seasonally open lagoons

Spatio‐temporal recruitment patterns, growth and survival of the Swan River goby Pseudogobius olorum and western hardyhead Leptatherina wallacei are described from two small, coastal lagoons on the south coast of Western Australia. In these lagoons, estuarine salinity dynamics were relatively stable over much of the autumn–spring period when freshwater inputs from rivers were reduced and there was no oceanic connection. Preflexion and flexion stages of both fish species contributed strongly to population size structure in downstream reaches, whereas upstream reaches were dominated by postflexion larvae and juvenile stages. Spawning of both species was protracted and largely asynchronous, although the episodic presence of stronger preflexion and flexion cohorts suggested some synchronized spawning had occurred. Comparison with estuarine conditions over this period provided evidence that synchronized spawning may be related to temperature and salinity variations from a combination of freshwater inputs and periods of marine exchange. Uninterrupted growth and the progression of cohorts through to juvenile stages were consistent with the generally stable estuarine conditions. Larval and juvenile stages of both species were also tolerant of abrupt changes in salinity and temperature, which occurred due to a non‐seasonal oceanic connection. These findings were consistent with the euryhaline nature of adults of both species.     

Effects of the river discharge management on the nursery function of the Guadalquivir river estuary (SW Spain)

Within the Guadalquivir estuary, young recruits of marine species seem to respond to changes in freshwater flow by moving with the mass of estuarine water that is most “suitable” for them. The control of the river flow, from a dam 110 km upstream from the river mouth, has an immediate effect on the estuarine salinity gradient, displacing it either seaward or upstream. Consequently, there is a reduction or enlargement of the estuarine area that is used as nursery grounds. The analysis of the temporal estuarine recruitment and spatial distribution of young stages of marine species, during six annual cycles, provides evidence that the estuarine zone used as nursery grounds is mainly that part situated seaward from an isohaline value of 5. The relationship between the position of that isohaline (D₅) and the freshwater discharges from the dam was also examined during high and low tides. It was found that a high percentage of the isohaline position variation (75% and 73% at high and low tides, respectively) can be explained by the freshwater volume discharged from the dam during the previous week. These preliminary results suggest that an accurate model of the relationship between these two variables may be a useful tool for future management strategies of freshwater discharges to the estuary.     

Biodiversity census of Lake St Lucia,iSimangaliso Wetland Park (South Africa): Gastropod molluscs

The recent dry phase experienced by the St Lucia estuarine system has led to unprecedented desiccation and hypersaline conditions through most of its surface area. This has changed only recently, at the end of 2011, with the onset of a new wet phase that has already caused a major shift to oligo- and mesohaline conditions. The estuary mouth, however, remains closed to the ocean, making the weak connection recently established between the St Lucia and the Mfolozi estuaries the only conveyance for marine recruitment. As a result, only 10 indigenous and two alien aquatic gastropod species are currently found living in the St Lucia estuarine lake. This is out of a total of 37 species recorded within the system since the earliest survey undertaken in 1924, half of which have not been reported in the literature before. The tick shell, Nassarius kraussianus, which was consistently found in large abundance prior to the recent dry phase, appears to have temporarily disappeared from the system, probably as a result of the extinction of Zostera marine grasses inside the lake. Population explosions of the bubble shell Haminoea natalensis, with its distinct egg masses, were recorded seasonally until 2009, but the species has subsequently not been observed again. A molecular DNA analysis of the various populations previously reported as belonging to the same assimineid species, variably referred to as Assiminea capensis, A. ovata, or A. bifasciata, has revealed that the St Lucia assemblage actually comprises two very distinct taxa, A. cf. capensis and a species provisionally referred to here as “A.” aff. capensis or simply Assimineidae sp. In the mangroves, the climbing whelk Cerithidea decollata is still found in numbers, while ellobiids such as Cassidula labrella, Melampus semiaratus and M. parvulus are present in low abundances and all previously recorded littorinids have disappeared. A number of alien freshwater species have colonized areas of the system that have remained under low salinity. These include the invasive thiarid Tarebia granifera, which can be found in concentrations exceeding 5000 ind.m^-2, the lymnaeid Pseudosuccinea columella and the physid Aplexa marmorata.     

Variations in the migratory history of the tropical catadromous eels Anguilla bicolor bicolor and A. bicolor pacifica in south-east Asian waters

Fish movements between aquatic habitats of different salinity ranges (fresh, estuarine, marine) by the tropical catadromous eels Anguilla bicolor bicolor and A. bicolor pacifica were examined by analysing the otolith strontium and calcium concentrations of yellow (immature) and silver (mature) stage eels collected in south-east Asian (Indonesia, Malaysia and Vietnam) waters. The ratios suggest that all migratory-type eels, including freshwater, brackish water and marine residents, pass the river mouth. However, the habitat preference was different among the sites (countries). In Indonesia and Vietnam, most A. bicolor bicolor and A. bicolor pacifica were either marine or brackish water residents in this study. Alternatively, most A. bicolor bicolor were freshwater residents in Malaysia; such a typical catadromous migration pattern in these eels has not been found in previous studies. The wide range of otolith Sr:Ca in both subspecies indicates that the habitat use of these tropical eels was opportunistic among fresh, brackish and marine waters during their growth phases following recruitment to coastal areas. The geographical variability of migratory histories suggests that habitat use might be determined by the inter and intraspecific competition and environmental conditions at each site.     

Occurrence of Gobiidae larvae in a tropical Brazilian estuary,with particular emphasis on the use of size classes to categorize species guilds

The structure and seasonal dynamics of larvae of the Gobiidae family in the Mucuri Estuary (Bahia, Brazil) were studied for nine consecutive years. Sampling was conducted at three stations in the lower estuary channel, between 2002 and 2010, in relation to season, day and night and tidal variations. A total of 5802 Gobiidae larvae, representing 15 taxa (12 species and three morphotypes), were collected in the Mucuri Estuary during this time. The highest mean ± s.d. density of fish larvae, 54·7 ± 79·8 larvae 100 m^?3, was recorded during the flood tide and night sampling. Ctenogobius boleosoma was the most abundant species (68%), being dominant in the rainy and dry seasons and had a long reproductive period. This species was classed as a marine estuarine‐opportunist because it was observed at high frequencies and active larvae entering the estuary between 6·1 and 12·0 mm standard length (L_S). Gobionellus oceanicus, second in abundance (12%), occurred only in later larval stages but did not use the estuary as a preferred location for spawning, being classed a marine estuarine dependent. Microgobius carri (11%) was represented in all L_S classes and was resident in the estuary for spawning, remaining there throughout their life cycle. The other species were considered rare due to their low densities and could not be classified in any guild.     

Morphology of the teleost ampullary organs in marine salmontail catfish Neoarius graeffei (Pisces: Ariidae) with comparative analysis to freshwater and estuarine conspecifics

We hypothesized that due to the relative conductivity of the environment, and to maintain sensory function, ampullary organs of marine Neoarius graeffei would differ morphologically from those described previously for estuarine and freshwater conspecifics. Unlike the ampullary systems of N. graeffei from freshwater and estuarine habitats, the ampullary pores of marine specimens occur in two distinct patterns; numerous pores seemingly randomly scattered on the head and ventro‐lateral regions of the body, and pores arranged in distinctive vertical lines above the lateral line on the dorso‐lateral body of the fish. Light and electron microscopy revealed that the ampullary organs also differed morphologically from estuarine and freshwater specimens in the presence of longer ampullary canals, a hitherto unreported canal wall composition, and in the collagen sheath surrounding both the canal and the ampulla proper within dermal connective tissues. Ampullary pores were wider in marine individuals and opened to the longest ampullary canals reported for this species. The canal wall was lined by cuboidal and squamous epithelial cells. Each ampullary canal opened into a single ampulla proper containing significantly more receptor cells than estuarine and freshwater conspecifics. The distribution of ampullary pores as well as the microstructure of the ampullary organs indicates that the electrosensory system of marine N. graeffei differs from those of estuarine and freshwater specimens in ways that would be expected to maintain the functionality of the system in a highly conductive, fully marine environment, and reveals the remarkable plasticity of this species’ ampullary system in response to habitat conductivity. J. Morphol. 276:1047–1054, 2015. © 2015 Wiley Periodicals, Inc.     

Sea‐level variations have influenced the demographic history of estuarine and freshwater fishes of the coastal plain of Paraná, Brazil

This study surveyed the mitochondrial haplotype diversity of nine freshwater fish species and two estuarine–marine species from the coastal basins and drainages of the highland plateaus of Paraná, Brazil. Portions of the cytochrome b gene or the control region were sequenced. The demographic history of each species was inferred using the Bayesian skyline method, mismatch distribution analysis and statistical neutrality tests. Demographic reconstruction analyses revealed a single pattern of variation in the effective population size (N_e) among species. No dramatic changes in N_e were detected in upland species. By contrast, evidence of population expansion over the past 200 000 years was detected in all coastal plain and estuarine species. These findings correspond to periods of low sea‐level (regressions) followed by a rapid increase in the sea‐level by >100 m. The resulting reconnections and subsequent fragmentation and isolation between the estuarine and freshwater bodies were putatively relevant to the historical demography of the fish species in these areas.     

Phytoplankton Fluctuations during an Annual Cycle in the Coastal Lagoon of Cullera (Spain)

The seasonal variation and the vertical distribution of the phytoplanktonic population of the lagoon of Cullera, an elongated coastal lagoon with estuarine circulation of water, has been studied in three sampling stations: mouth, centre and source. Seasonal variation is determined by a marine-freshwater interaction. In winter, the sea influence is important, a marine water wedge of anoxic water arrives at the sampling station located at the source and marine and brackish water species dominate the phytoplankton. Also marine species of zooplankton and fish enter the system, which may then be considered as exploited by the sea. In spring the marine wedge retreats from the source but remains in the centre and mouth, salinity diminishes, vertical mixing persists and phytoplankton is dominated by Cyclotella species. From late spring to autumn the freshwater influence prevails and a sharp stratification of the water is produced in the stations at the mouth and the centre, by means of a steep halocline coincident with an oxycline. The phytoplankton in this period follows a typical succession like those described in freshwater eutrophic lakes. Vertical distribution of phytoplankton is determined by the presence of the oxycline, originated by the marine water wedge, whose depth varies seasonally but which is always present in the mouth and centre of the lagoon; only few species of algae can be found below its level.     

Biogeography,habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

Rivers and lake systems in the southern cone of South America have been widely influenced by historical glaciations, carrying important implications for the evolution of aquatic organisms, including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via waterway connectivity and stream capture events. Silverside fishes (Odontesthes) in the region comprise a radiation of 19 marine and freshwater species that have been hypothesized on the basis of morphological or mitochondrial DNA data to have either transitioned repeatedly into continental waters from the sea or colonized marine habitats following freshwater diversification. New double digest restriction‐site associated DNA data presented here provide a robust framework to investigate the biogeographical history of and habitat transitions in Odontesthes. We show that Odontesthes silversides originally diversified in the Pacific but independently colonized the Atlantic three times, producing three independent marine‐to‐freshwater transitions. Our results also indicate recent introgression of marine mitochondrial haplotypes into two freshwater clades, with more recurring instances of hybridization among Atlantic‐ versus Pacific‐slope species. In Pacific freshwater drainages, hybridization with a marine species appears to be geographically isolated and may be related to glaciation events. Substantial structural differences of estuarine gradients between these two geographical areas may have influenced the frequency, intensity and evolutionary effects of hybridization events.