The accurate evaluation of population structure is a serious challenge for the effective management and conservation of many highly migratory fish species, including albacore tuna (Thunnus alalunga). Albacore occur throughout most temperate and tropical ocean waters around the world, supporting large fisheries of particular economic important to many regions. Albacore are capable of swimming continuously at high speeds and traveling vast distances within their lifetime, but surprisingly little is known about the distribution, migration cycle, and population structure of the species. This lack of knowledge is a concern as annual landings for albacore are highly variable, and recent research predicts that the range of the species will be significantly affected by climate change. We use double-digest restriction-site associated DNA (ddRAD) sequencing to investigate the population genetic variation among albacore in the Pacific Ocean, and test for neutral and putatively adaptive genetic differences among groups. We sample hundreds of albacore from 2 areas in the South Pacific and 10 areas in the North Pacific, including 6 locations along the West Coast. Our results challenge conclusions based on previous small-scale genetic and tagging studies, and we suggest topics for future research.