The recognition of bull troutSalvelinus confluentusand Dolly VardenS. malmaas separate species is a contentious issue in the state of Washington. Our analysis of 47 protein-coding loci indicated that at 5 loci fixed genetic differences exist between these species in the Olympic Peninsula and Puget Sound area of Washington. Samples from two Olympic Peninsula and two Puget Sound rivers contained only bull trout. A sample from a third Puget Sound river contained only Dolly Varden. A sample from a third Olympic Peninsula river contained both bull trout and Dolly Varden, but no evidence of hybridization or introgression existed. These results indicate these species are distinct and Sympatric in western Washington, and hybridization between them is not common. Thus, these fishes should be managed as separate species.