Chinook Salmon Oncorhynchus tshawytscha exhibit substantial population genetic structure at multiple scales. Although geography is generally more important than life history, particularly migration and run timing, for describing genetic structure in Chinook Salmon, there are several exceptions to this general pattern, and hatchery supplementation has altered natural genetic structure in some areas. Given that genetic structure of Chinook Salmon is often basin-specific, we assessed genetic variation of 27 microsatellite loci in geographically and temporally distinct natural populations and hatchery stocks in the Klamath River basin, California. Multiple analyses support recognition of three major genetic lineages from separate geographic regions in the Klamath River basin: the lower basin, the Klamath River, and the Trinity River. The lower basin group was sharply distinct, but populations in the Klamath and Trinity river lineages were connected by processes that can be described by a one-dimensional, linear, stepping-stone model where gene exchange occurred primarily, but not exclusively, between adjacent populations. Genetic structure by migration timing was also evident, although divergences among populations that differed by migration timing only were fewer than those observed between geographic regions. Distinct run-timing ecotypes in the Klamath River basin thus appear to have evolved independently through a process of parallel evolution. Introgressive pressure from the
hatchery stocks into natural populations was attenuated by distance from the hatchery, but comparison of historical population genetic structure to contemporary patterns would be needed to fully evaluate the extent to which hatchery stocks may have altered natural genetic structure.