The fauna of fish parasites in Lake Baikal is represented by 5 faunistic complexes, namely the boreal plain, boreal submountain, arctic freshwater, Baikal, and Sino-Indian ones. The parasites of the boreal plain complex are dominant by the number of species (43 %). Hypotheses on the origin of the recent fish and parasite faunas of Lake Baikal were advanced on the base of the data on the parasite species composition and their distribution among hosts, as well as on the base of paleontological data. It is shown that invasion of new fish species and their parasites to Baikal led to the change of the composition of natural faunistic fish complexes and parasite systems. Invading fishes play the roles of intermediate and definitive hosts in parasite systems of Baikal, that led to the change of the initial structure of these systems.