Located in the Pacific Northwest, the Columbia River basin provides important spawning and rearing habitat for Pacific salmon and steelhead (Oncorhynchus spp.). These species were historically abundant throughout the basin but have experienced extensive declines linked to a complex suite of factors. These declines, in tandem with their cultural and economic significance, have led Pacific salmon and steelhead to become one of the most intensely managed groups of species in North America. Management actions have increasingly recognized the importance of genetic resources and have expanded the use of genetic tools to provide powerful data for the conservation and management of Pacific salmon. We provide a summary of historic management actions in the basin with a focus on those relevant to genetic applications. We describe the initial recognition of genetic differences and distinction of population units, how genetics applies to the hatchery controversy, as well as the progression of genetic investigations and applications used in management. Further, we outline some emerging and potential future genetic tools.