Understanding diet is critical for conservation of endangered predators. The Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily in the west coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of the whales’ seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook salmon (Oncorhynchus tshawytscha), despite this species’ rarity compared to some other salmonids. During other times of year, when ranging patterns include the U.S. and Canadian west coast and the northern and southern portions of the Salish Sea, their diet is largely unknown. To address this data gap, we collected feces and prey remains from October to May 2004-2017 in both the Salish Sea and U.S. west coast waters. Using visual and genetic species identification for prey remains and genetic approaches for fecal samples, we characterized the diet of the SRKWs in fall, winter, and spring. Chinook salmon were identified as an important prey item year-round, averaging ~50% of their diet in the fall, increasing to 70-80% in the late winter/early spring, and returning to nearly 100% in the late spring. Other salmon species and non-salmonid fishes, also made substantial dietary contributions.  The relatively high species diversity in winter suggested a possible lack of Chinook salmon, probably due to seasonally lower densities, based on their proclivity to selectively consume this species in other seasons. A wide diversity of Chinook salmon stocks were consumed, many of which are also at risk. Although west coast samples consisted of 14 stocks, four rivers systems accounted for 90% of the samples, predominantly the Columbia River. Increasing the abundance of Chinook salmon stocks that inhabit the whales’ winter range may be an effective conservation strategy for this population.

There are 52 fasta files containing DNA sequences from a ~330bp fragment of the mitochondrial 16s ribosomal RNA gene. These sequences were amplified from killer whale feces collected from the wild. The file names correspond to the sample pools described in Table S5 of the associated publication which contains sampling information (time, location, whale ID if known). In addition to the experimental samples, there are 9 control samples, as described in Table S4 of the publication. Methodological details including primers and sequencing methods are described in the associated publication.