The population structure of the Baltic salmon (Salmo salar) specific clade of Gyrodactylus salaris was studied using mitochondrial and nuclear DNA markers across a gradient of historical coadaptation. In the Onega and Ladoga lakes, the salmon was near to eliminating the parasite: just 5 of 548 inspected salmon juveniles carried a small number of parasites. In the northern Baltic Tornio River, G. salaris was observed as non-pathogenic in 23% of 765 fish. The population of naïve anadromous salmon in the Keret' River (White Sea) had almost perished after the parasite was imported from Lake Onega in 1992. The parasite clones defined by mtDNA were strongly spatially structured (F_ST = 0.548 in Keret'; F_ST = 0.484 in Tornio), suggesting competitive interactions via host defense. The prevalence and clonal structuring of G. salaris were concordant with the host resistance predicted from the suggested 132 000 years of common phylogeographic history in the Baltic refugia.