The distribution of the freshwater myxozoan parasite Ceratonova shasta in the Pacific Northwest of North America is limited to overlap in the ranges of its 2 hosts: the polychaete Manyunkia sp., and Pacific salmonids. Studies in the Klamath River (Oregon/California) and Deschutes River (Oregon), showed that the parasite population is comprised of multiple sympatric genotypes, some of which correlate with particular salmonid host species and with differences in clinical disease in those hosts. The 3 primary genotypes O, I, and II are defined by the number of a specific tri-nucleotide repeat in the internal transcribed spacer-1 region. To understand the spatial extent of host–parasite genotype patterns, we sequenced the parasite from 448 salmonid fishes from river basins in California, Oregon, Washington, Idaho, and British Columbia, Canada. We sampled intestinal tissues from 6 species of salmon and trout, both those that exist naturally with the parasite (sympatric) and those that do not naturally co-occur with the parasite and were exposed artificially in cages (allopatric). In most river basins we detected the same primary C. shasta genotypes that were described from the Klamath and Deschutes rivers, and we did not detect any novel primary genotypes. Host–parasite genotype patterns were consistent with previous data: genotype O was found in sympatric trout only; genotype I predominantly in Chinook salmon, and genotype II in all 6 fish species but dominant in coho salmon. Our findings of widespread, consistent host–parasite genotype patterns support the hypothesis that C. shasta has a long evolutionary history with salmonid fishes in the Pacific Northwest, and impels additional studies to determine if these parasite genotypes should be considered different species.