Influence of aperiodic summer droughts on leaf litter breakdown and macroinvertebrate assemblages: testing the <Emphasis Type="Italic">drying memory</Emphasis> in a Central Apennines River (Aterno River,Italy)

Management of multiple exploited stocks of anadromous salmonids in large catchments requires understanding of movement and catchment use by the migrating fish and of their harvesting. The spawning migration of sea trout (Salmo trutta) and Atlantic salmon (Salmo salar) was studied in the River Tweed, UK, using acoustic telemetry to complement exploitation rate data and to quantify catchment penetration. Salmon (n = 79) and sea trout (n = 65) were tagged in the tidal-influenced Tweed in summer–autumn. No tagged salmon left the river before spawning, but 3% (2010) and 8% (2011) of pre-spawning sea trout dropped out. Combined tag regurgitation/fish mortality in salmon was 12.5%, while trout mortality was 6% (2010) and 0% (2011). The estimated spawning positions of salmon and sea trout differed; tagged salmon were mostly in the main channel while trout occurred mostly in the upper Tweed and tributaries. Early fish migrated upstream slower than later fish, but sea trout moved through the lower-middle river more quickly than salmon, partly supporting the hypothesis that the lower exploitation rate in autumn of trout (1 vs 3.3% for salmon) there is generated by differences in migration behaviour.     

Thermal biology and bioenergetics of different upriver migration strategies in a stock of summer-run Chinook salmon

By combining biotelemetry with animal-borne thermal loggers, we re-created the thermal histories of 21 summer-run Chinook salmon (Oncorhynchus tshawytscha) migrating in the Puntledge River, a hydropower impacted river system on Vancouver Island, British Columbia, Canada. Daily maximum water temperatures in the Puntledge River during the summer-run adult Chinook salmon migration and residency period frequently exceeded 21 °C, a value that has been observed to elicit behavioral thermoregulation in other Chinook salmon populations. We therefore compared river temperatures to body temperatures of 16 fish that migrated through the river to understand if cool-water refuge was available and being used by migrants. In addition, we used thermal histories from fish and thermal loggers distributed in the river to model the effect of thermal habitat on energy density using a bioenergetics model. In general, we found no evidence that cool-water refuge existed in the river, suggesting that there is no opportunity for fish to behaviorally thermoregulate during upriver migration through the regulated portion of the river. Of the thermal histories used in the bioenergetics model, fish that reached an upstream lake were able to access cooler, deeper waters, which would have reduced energy consumption compared to fish that only spent time in the warmer river. Consequently, the Puntledge River water temperatures are likely approaching and in some cases exceeding the thermal limits of the summer-run Chinook salmon during the spawning migration. Further warming may cause more declines in the stock.     

Characteristics of the spawning stock of chinook salmon <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis> from the Apuka River (northeastern Kamchatka)

Biological features of chinook salmon Oncorhynchus tshawytscha from the Apuka River, the largest river of the northeastern Kamchatka inflowing Olyutorskii Bay of the Bering Sea, are studied. Chinook salmon from the Apuka River spend mainly a year in the river before downstream migration to the sea. The fish live in the sea for 1–4 years. The spawning migration of chinook salmon into the Apuka River begins in late May just after ice melting, and it continues until early August. The main part of the spawners enters the river during June. A hypothesis on the occurrence of two seasonal races in the Apuka River is proposed.     

A century of Chinook salmon consumption by marine mammal predators in the Northeast Pacific Ocean

As many marine mammal populations have increased following bans on their harvest, there has been a growing need to understand potential impacts of these population changes on coastal marine ecosystems. Quantifying consumption of prey species, such as fish, is particularly important when those same prey are also targeted by commercial fisheries. Estimating the impact of marine mammal predators on prey fish depends upon knowledge of marine mammal diet composition; scientific advances over the last century have improved understanding of diets but have also led to inconsistent methods that challenge attempts at synthesis and comparison. Meta-analysis techniques offer the opportunity to overcome such challenges, yet have not been widely applied to synthesize marine mammal diets over space and time. As a case study, we focus on synthesizing diet studies of Chinook (king) salmon (Oncorhynchus tshawytscha) by four species of marine mammal predators in the Northeast Pacific Ocean: Steller sea lions (Eumetopias jubatus), California sea lions (Zalophus californianus), harbor seals (Phoca vitulina), and killer whales (Orcinus orca). We also highlight several simple meta-analyses for which these types of diet databases may be employed. Our assembled database consists of > 330 records, spanning more than 100 years. Results indicate that the frequency of occurrence of Chinook salmon in killer whale studies is high (63%) relative to pinniped studies (< 10%). They also suggest a strong increasing ability to discriminate Chinook salmon from other salmonids, which we attribute to switches in diet studies from lethal or observational sampling toward molecular methods (DNA, fatty acids). Our database and analysis code are published as supplementary material, which we hope will be useful for other researchers and will inspire more of these syntheses.     

Upstream passage problems for wild Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis> L.) in a regulated river and its effect on the population

Due to hydropower development, the upstream migration of wild anadromous salmon and brown trout is impaired in many European rivers, causing negative effects on the long-term survival of natural salmonid populations. This study identified problems for Atlantic salmon during upstream migration in a regulated river in northern Sweden, Umeälven (mean flow: 430 m³ s^?1). Tagging from 1995 to 2005 involved radio tags (n = 503), PIT tags (n = 1574) and Carlin tags (n = 573) to study the spawning migration of salmon from the coast past the regulated section of the river to a fish ladder at the dam/spillway 32 km upriver. The results demonstrate that migration success from the coast to the fish ladder varied between 0% and 47% among years, indicating an average loss of 70% of potential spawners. Discharge from the turbines attracted the salmon away from the bypass route. Echo-sounding in the turbine outlet showed that salmon were normally found at 1–4 m depths. They responded with upstream and/or downstream movements depending on flow changes; increased spill in the bypass channel attracted salmon to the bypass. Once in the bypass channel, salmon could be delayed and had difficulties passing the first rapid at high spills. Additional hindrances to upstream migration were found at rapids and the area of the fish ladder, located further upstream in the regulated river section. The average migration duration was 44 days from the estuary to the top of the fish ladder, with large variation among individuals within years. Modelling the salmon population dynamics showed a potential population increase of 500% in 10 years if the overall migration success could be improved from the current 30% to levels near 75%. Consequently improved migration facilities at the regulated river section should be implemented to achieve a long-term sustainability of these threatened anadromous salmonids.     

Upstream migration rates of radio‐tagged adult Chinook salmon in riverine habitats of the Columbia River basin

Upstream migration rates were assessed for 1801 radio‐tagged adult spring–summer Chinook salmon Oncorhynchus tshawytscha through 12 unimpounded river reaches in the Columbia River basin from 1997 to 2002. Reaches were 36 to 241 km long (mean = 130 km) and included sections of the large Columbia and Snake Rivers and smaller free‐flowing tributaries. Median Chinook salmon migration rates ranged from <10 km day⁻¹ in the Deschutes and Clearwater Rivers to >35 km day⁻¹ in the Columbia and Snake Rivers. Using multivariate analyses, migration date explained the most variance in Chinook salmon migration rates while river discharge, migration year and migration reach were secondary. Both within and between years, Chinook salmon migrated more rapidly as migration date increased and more slowly when discharge was high. Arrival at high elevation spawning grounds at appropriate times and increased metabolic activity and reproductive maturation may explain the greater power of migration date, relative to river discharge, in predicting migration rates of Columbia basin spring–summer Chinook salmon.     

Context-dependent diel behavior of upstream-migrating anadromous fishes

Variability is a hallmark of animal behavior and the degree of variability may fluctuate in response to environmental or biological gradients. For example, diel activity patterns during reproductive migrations often differ from those in non-breeding habitats, reflecting trade-offs among efficient route selection, reproductive phenology, and risk avoidance. In this study, we tested the hypothesis that diel movements of anadromous fishes differ among freshwater migration habitats. We analyzed diel movement data from ~13 000 radio-, PIT-, and acoustic-tagged adult fishes from five Columbia River species: Chinook salmon, Oncorhynchus tshawytscha; sockeye salmon, O. nerka; steelhead, O. mykiss; Pacific lamprey, Entosphenus tridentatus; and American shad, Alosa sapidissima. All five species were active during most of the diel cycle in low-gradient, less hydraulically complex reservoir and riverine habitats. Movement shifted to predominantly diurnal (salmonids and American shad) or nocturnal (Pacific lamprey) at hydroelectric dam fishways where hydraulic complexity and predator density were high. Results suggest that context-dependent behaviors are common during fish migrations, and that diel activity patterns vary with the degree of effort or predation risk required for movement.     

Juvenile Chinook salmon,Oncorhynchus tshawytscha,use of the Elwha river estuary prior to dam removal

The estuary of the Elwha River, on Washington’s Olympic Peninsula, has been degraded and simplified over the past century from sediment retention behind two large dams, levee construction, and channelization. With the removal of Elwha Dam and initiation of Glines Canyon Dam’s removal in fall 2011, sediment deposits will change the estuary and affect anadromous and nearshore marine fishes. Juvenile Chinook salmon commonly use estuaries and the river’s population is part of an Evolutionarily Significant Unit listed as Threatened under the U.S. Endangered Species Act. This study reports on monthly sampling in part of the river’s estuary from March 2007 through September 2011 to characterize the seasonal changes in relative abundance of yearlings and sub-yearlings, and size distributions prior to dam removal. Most (69 %) of the yearlings were caught in April, when this life history type was released from the hatchery, and to a lesser extent in May (28 %) and June (3 %). Yearlings caught in the estuary were smaller than those released from the hatchery (means: 153 mm?±?28 SD vs. 175 mm?±?5 SD), suggesting more rapid departure by larger fish. Sub-yearlings were much more abundant in the estuary, and were caught from March through November, increasing in mean fork length by 8.7 mm month^-1. The hatchery-origin sub-yearlings were not marked externally and so were not distinguishable from natural origin fish. However, 39 % of the sub-yearlings were caught prior to June, when sub-yearlings were released from the hatchery, indicating substantial use of the estuary by natural-origin fish. Thus, even in a reduced state after a century of dam operation, the highly modified estuary was used over many months by juvenile Chinook salmon. The information on juvenile Chinook salmon prior to dam removal provides a basis for comparison to patterns in the future, when the anticipated increase in estuarine complexity may further enhance habitat use by juvenile Chinook salmon.     

Fish habitat use response to anthropogenic induced changes of physical processes in the Elwha estuary, Washington, USA

The Elwha River estuary has been significantly influenced by anthropogenic changes to the river, including two large dams upriver and rock dikes installed in the estuary. Together these have disrupted hydrodynamic processes and subsequent sediment delivery throughout the watershed. This article defines the functional response of fish distribution within the estuary as a result of these changes. We assessed fish distribution of three main areas of the Elwha estuary using standard beach seining techniques from March to August 2007. Species composition, ecological indices, and relative proportion of all salmonids, and in particular Chinook salmon (Oncorhynchus tshawytscha), were consistently significantly different across the estuary. Differences corresponded to a rock dike installed 30 years ago, and a sediment lens that was observed to form at the entrance to the east estuary. Sediment lenses are documented to be a common occurrence in the Elwha nearshore, and symptomatic of documented, severely disrupted sediment processes of the Elwha River. Combining the fish distribution documented in this study with the rock dike and observed sediment lens and the sediment processes documented by other researchers we, therefore, conclude: (1) Fish use within the Elwha River estuary is complex, and even fragments of connected estuary are critically important for migrating salmon; (2) Anthropogenic effects, including in river damming and diking of the estuary, can be an important ecological driver in nearshore habitat function that should be appropriately considered in estuary habitat research, management, and restoration; and (3) Juvenile salmonids appear to be able to respond to dynamic sediment environments if there are habitat options available.     

Effects of predator and flow manipulation on Chinook salmon (Oncorhynchus tshawytscha) survival in an imperiled estuary

We evaluated the effects of non-native, piscivorous fish removal and artificial flow manipulation on survival and migration speed of juvenile Chinook salmon, Oncorhynchus tshawytscha, emigrating through the eastern Sacramento-San Joaquin Delta of California (Delta) using a Before-After-Control-Impact study design. Acoustically-tagged salmon survival increased significantly after the first predator reduction in the impact reach. However, survival estimates returned to pre-impact levels after the second predator removal. When an upstream control gate opened (increasing flow and decreasing tidal effect) juvenile salmon emigration time decreased and survival increased significantly through the impact reach. Though a short-term, single season experiment, our results demonstrate that predator control and habitat manipulation in the Delta tidal transition zone can be effective management strategies to enhance salmon survival in this highly altered system.     

Short‐term response of fish communities and water chemistry to breaching of a causeway in the Sarita River Estuary,British Columbia,Canada

On the west coast of Vancouver Island, Canada, in the Treaty Settlement Lands of the Huu‐ay‐aht First Nation, a causeway isolating the southern portion of the Sarita River estuary was breached in 2018 to enhance juvenile salmon and tidal water access into the southern portion of the estuary. Short‐term goals of breaching were to: (1) enhance juvenile salmon access through the causeway; (2) promote colonization of Chinook and Chum Salmon in pools, while retaining Coho Salmon; (3) monitor the entire estuary fish community, including non‐salmonids, to assess breaching success; and (4) homogenize water chemistry in pool and channel ecosystems currently fragmented by the causeway. Immediately following the breach, both fish community and water chemistry measurements indicate that these goals were achieved. Chinook and Chum Salmon utilization increased inside and outside of the causeway following breaching. Similarly, Chinook and Chum salmon were observed in pool ecosystems, and Coho Salmon were also retained in pools following breaching. Water chemistry was homogenized post‐breach, primarily due to increased saltwater penetration. While continued monitoring is required, short‐term indicators suggest that breaching was effective in increasing connectivity of the Sarita Estuary, allowing access to 1.4 km² of habitat that had previously been inaccessible to juvenile salmon.     

Survival of captured and relocated adult spring-run Chinook salmon Oncorhynchus tshawytscha in a Sacramento River tributary after cessation of migration

We studied the efficacy of the process for capture and upstream relocation of 26 adult spring-run Chinook salmon in Butte Creek, California in 2009. These fish had ceased volitional upstream migration prior to reaching their summer holding habitat. The purpose of the relocation was to move fish upstream of two water diversion dams and release them in a part of the stream from which they could presumably swim to cool summer holding habitat, then spawn in the fall. Fish were netted, transported by truck, given an esophageal radio tag/temperature tag, and released. Radio tagging proved to be a useful technique for determining the survival and movement of relocated fish and temperature tags provide useful information to determine thermal exposure and time of death. Twenty-three tags (88 %) were recovered, compared with a 10 % tag recovery rate for an earlier study using fin clips. Most tags were recovered within 3.5 km upstream and 1 km downstream of the release site. A single tag was recovered 6 km upstream. No fish were determined to have survived to spawn. Temperature tag data indicate that most of the salmon died within 2–6 days after the relocation operation. After preventative measures have been exhausted, future relocations efforts, in any setting, should consider (1) intervention as soon as fish cease volitional migration but before they are exposed to further deleterious conditions (2) monitoring environmental conditions to choose appropriate release sites (3) evaluation of disease transmission risk, and (4) handling practices that minimize potential stress due to air immersion and thermal shock.     

Can non-native smallmouth bass, <Emphasis Type="Italic">Micropterus dolomieu</Emphasis>, be swamped by hatchery fish releases to increase juvenile Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, survival?

One of the strategies that can be used to reduce predation impacts to valued fish species is by swamping predators with more prey than they can eat. We examined whether this approach was viable by calculating the maximum bioenergetic consumption potential of non-native smallmouth bass Micropterus dolomieu on fall Chinook salmon Oncorhynchus tshawytscha juveniles in the Yakima River throughout the spring between 1998 and 2002 and comparing those estimates to previously published estimates of fall Chinook salmon consumption. We found that the smallmouth bass population consumed fall Chinook salmon well below their bioenergetic potential. However, individual smallmouth bass that were piscivorous were eating other food items at a level near satiation. Furthermore, the maximum consumption potential was relatively low prior to mid-April, and then increased substantially to a peak in May. Predation mortality to hatchery fall Chinook salmon could be reduced within a year by releasing hatchery fall Chinook salmon that will emigrate quickly prior to mid-April, when predation potential is still very low. However, attempting to swamp predators with hatchery Chinook salmon to benefit naturally produced Chinook salmon poses uncertain benefits to natural origin fish and likely unacceptable costs to hatchery fish. Considerable swamping is occurring by other naturally produced fish species in the Yakima River such as dace Rhinichthys spp., mountain whitefish Prosopium williamsoni, and crayfish Pacificastus spp. Therefore, it is important to consider impacts to these non-target species because they could have indirect predation impacts on Chinook salmon.     

Return migration of Atlantic salmon in the River Tana: the role of environmental factors

Multi-sea-winter Atlantic salmon (75–115 cm fork length L _F, 2–4-winter fish) were radio-tagged in the Tanafjord (700 N), Norway, in 1992–1993, and 130 fish entered the large subarctic River Tana (Teno). They entered the fresh water at any time of the tidal cycle but more so during the high and ebbing tides. No diel rhythm was detected in river entry under polar day conditions. There were no differences in the change of flow between days when salmon moved and when they did not, but during active migration increasing discharge was associated with increased swimming activity of salmon, especially later in the summer. Increasing air temperature was also associated with enhanced migration activity. Low river flow was associated with increasing delay in salmon passing the first riffle area of the river, 35 km from the sea.     

Diel movements of out-migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) smolts in the Sacramento/San Joaquin watershed

We used ultrasonic telemetry to describe the movement patterns of late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) smolts during their entire emigration down California’s Sacramento River, through the San Francisco Bay Estuary and into the Pacific Ocean. Yearling hatchery smolts were tagged via intracoelomic surgical implantation with coded ultrasonic tags. They were then released at four upriver locations in the Sacramento River during the winters of 2007 through 2010. Late-fall run Chinook salmon smolts exhibited a nocturnal pattern of migration after release in the upper river. This is likely because individuals remain within a confined area during the day, while they become active at night and migrate downstream. The ratio between night and day detections of Chinook salmon smolts decreased with distance traveled downriver. There was a significant preference for nocturnal migration in every reach of the river except the Estuary. In contrast, steelhead smolts, which reside upriver longer following release, exhibited a less pronounced diel pattern during their entire migration. In the middle river, Delta, and Estuary, steelhead exhibited a significant preference for daytime travel. In the ocean Chinook salmon preferred to travel at night, yet steelhead were detected on the monitors equally during the night and day. These data show that closely related Oncorhynchus species, with the same ontogenetic pattern of out-migrating as yearlings, vary in migration tactic.     

Effect of origin, sex and sea age of Atlantic salmon on their recapture rate after river ascent

The recapture rate of Atlantic salmon (Salmo salar L.) after river ascent was examined by the trapping and tagging of ascending spawners in the lower reaches of the Simojoki River, which flows into the northern Baltic Sea. In 1997 and 1998, altogether 825 Carlin‐tagged salmon were released to continue their upstream migration. Of these, 800 could be sexed and categorized as reared (91%) or wild (9%) salmon. In 1997, most of the ascending salmon were multi‐sea‐winter (MSW) fish, whereas in 1998 almost all were one‐sea‐winter (1SW) male grilse due to the late trapping season. About 10% of all tagged fish were recaptured, two‐thirds of which were caught in the river before their descent to the sea. There was no difference in the recapture rate between salmon of wild (8.5%) or reared (9.5%) origin, or between females (11.6%) and males (9.3%). Generalized linear models for data from 1997 showed that the recapture rate increased with length and age of females, but that the opposite was true for males. River fishing did not seem to remove proportionally more early ascending salmon than fish that ascended later.     

Invasion of Ceratomyxa shasta (Myxozoa) and comparison of migration to the intestine between susceptible and resistant fish hosts

The myxozoan parasite Ceratomyxa shasta infects salmonids causing ceratomyxosis, a disease elicited by proliferation of the parasite in the intestine. This parasite is endemic to the Pacific Northwest of North America and salmon and trout strains from endemic river basins show increased resistance to the parasite. It has been suggested that these resistant fish (i) exclude the parasite at the site of invasion and/or (ii) prevent establishment in the intestine. Using parasites pre-labeled with a fluorescent stain, carboxyfluorescein succinimidyl diacetate (CFSE), the gills were identified as the site of attachment of C. shasta in a susceptible fish strain. In situ hybridization (ISH) of histological sections was then used to describe the invasion of the parasites in the gill filaments. To investigate differences in the progress of infection between resistant and susceptible fish, a C. shasta-susceptible strain of rainbow trout (Oncorhynchus mykiss) and a C. shasta-resistant strain of Chinook salmon (Oncorhynchus tshawytscha) were sampled at consecutive time points following exposure at an endemic site. Using ISH in both species, the parasite was observed to migrate from the gill epithelium into the gill blood vessels where replication and release of parasite stages occurred. Quantitative PCR verified entry of the parasite into the blood. Parasite levels in blood increased 4 days p.i. and remained at a consistent level until the second week when parasite abundance increased further and coincided with host mortality. The timing of parasite replication and migration to the intestine were similar for both fish species. The field exposure dose was unexpectedly high and apparently overwhelmed the Chinook salmon’s defenses, as no evidence of resistance to parasite penetration into the gills or prevention of parasite establishment in the intestine was observed.     

Juvenile salmon in estuaries: comparisons between North American Atlantic and Pacific salmon populations

All anadromous fishes, including juvenile salmon, encounter estuarine habitats as they transition from riverine to marine environments. We compare the estuarine use between juvenile Atlantic salmon (Salmo salar) in the Penobscot River estuary and Pacific salmon (Oncorhynchus spp.) in the Columbia River estuary. Both estuaries have been degraded by anthropogenic activities. Atlantic and Pacific salmon populations in both basins rely heavily on hatchery inputs for persistence. Pacific salmon, as a group, represent a continuum of estuarine use, from species that move through rapidly to those that make extensive use of estuarine habitats. While Atlantic salmon estuarine use is predominantly similar to rapidly moving Pacific salmon, they can exhibit nearly the entire range of Pacific salmon estuarine use. Both slow and rapidly migrating Atlantic and Pacific salmon actively feed in estuarine environments, consuming insect and invertebrate prey. Interactions between juvenile salmon and estuarine fish communities are poorly understood in both estuaries, although they experience similar avian and marine mammal predators. Estuaries are clearly important for Atlantic and Pacific salmon, yet our understanding of this use is currently insufficient to make informed judgments about habitat quality or overall estuary health. This review of salmonid migration through and residency within estuaries identifies actions that could hasten restoration of both Atlantic and Pacific salmon populations.     

Indirect Effects of Impoundment on Migrating Fish: Temperature Gradients in Fish Ladders Slow Dam Passage by Adult Chinook Salmon and Steelhead

Thermal layering in reservoirs upstream from hydroelectric dams can create temperature gradients in fishways used by upstream migrating adults. In the Snake River, Washington, federally-protected adult salmonids (Oncorhynchus spp.) often encounter relatively cool water in dam tailraces and lower ladder sections and warmer water in the upstream portions of ladders. Using radiotelemetry, we examined relationships between fish passage behavior and the temperature difference between the top and bottom of ladders (∆T) at four dams over four years. Some spring Chinook salmon (O. tshawytscha) experienced ∆T ≥ 0.5 °C. Many summer and fall Chinook salmon and summer steelhead (O. mykiss) experienced ∆T ≥ 1.0 °C, and some individuals encountered ΔT > 4.0°C. As ΔT increased, migrants were consistently more likely to move down fish ladders and exit into dam tailraces, resulting in upstream passage delays that ranged from hours to days. Fish body temperatures equilibrated to ladder temperatures and often exceeded 20°C, indicating potential negative physiological and fitness effects. Collectively, the results suggest that gradients in fishway water temperatures present a migration obstacle to many anadromous migrants. Unfavorable temperature gradients may be common at reservoir-fed fish passage facilities, especially those with seasonal thermal layering or stratification. Understanding and managing thermal heterogeneity at such sites may be important for ensuring efficient upstream passage and minimizing stress for migratory, temperature-sensitive species.     

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population’s summer diet.