The long-term dynamics of the parasitic infection of two coregonid species with different food specializations, peled Coregonus peled (Gmelin, 1789) and Siberian whitefish Coregonus lavaretus pidschian (Gmelin, 1788), during spawning migration in the Synya River (a Polar Urals tributary of the Lower Ob) has been studied. The differences in the parasite species composition and infection of the two fish species are determined their food spectra features, as well as by their use of different biotopes in feeding water bodies and the interannual dynamics of the fish age composition. A trend towards a decrease in the rate of peled infection by myxosporidium and cestode with a simultaneous decrease in its abundance due to intensive catches has been revealed. The stability of the composition of the coregonid parasite fauna in the Ob lower reaches indicates stable relationships between parasites and hosts and a relatively stable state of the ecosystem of the Lower Ob.