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Using different classes of genetic markers can provide insight into the role of selection, as well as a broader context for identifying population differentiation. We used nine microsatellite loci and polymorphisms at eight gene loci (major histocompatibility complex (MHC) classes I and II, growth hormones 1 and 2, transferrin, and immunoglobin heavy-chain) to determine population structure in six coastal populations (Vancouver Island, VI) and five interior populations (Fraser River, FR) of Chinook salmon (Oncorhynchus tshawytscha) in British Columbia, Canada. FST and [Formula: see text] values for specific VI gene loci were significantly higher than those for the FR and VI microsatellite loci or the FR gene loci. Pairwise microsatellite FST values were correlated with geographic distance across regions, but not using the gene locus marker data. Neighbor-joining cluster analyses showed one VI population as particularly divergent based on the gene locus data, while the VI and FR microsatellite locus and the FR gene locus analyses yielded no anomalous population divergence. The VI MHC class II marker FST values were exceptionally high, indicative of probable directional selection acting on MHC class II. Our results are consistent with local adaptation in Chinook salmon, but the nature of the local adaptation likely differs among regions.

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