We genotyped Chinook salmon (Oncorhynchus tshawytscha) from the Bering Sea and North Pacific Ocean for 43 single-nucleotide polymorphisms (SNPs) to investigate seasonal distribution and migration patterns. We analyzed 3563 immature fish from 22 spatiotemporal strata; composition analyses were performed using genotype data from spawning stocks spanning the species range. Substantial variation in stock composition existed among spatial and seasonal strata. We inferred patterns of seasonal migration based upon these data along with data from previous tag, scale, and parasite studies. We found that stocks from western Alaska and Yukon River overwinter on the Alaska continental shelf then travel to the middle and western Bering Sea during spring-fall. Stocks from California to Southeast Alaska were distributed in Gulf of Alaska year-round, with a substantial portion of this group migrating northward to the eastern Bering Sea during spring-fall. Proportions of Russian stocks increase when moving east to west in both the Bering Sea and North Pacific Ocean. These data can be used to better understand the impacts of fisheries and climate change on this valuable resource.