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Changes in the numbers of 10 species of parasites belonging to 5 classes of roach and Siberian dace were investigated in the transect "Selenga River -Delta -Lake Baikal" in 2001Baikal" in -2006. The numbers either increased along this transect (myxosporea Myxobolus bramae, monogeneans of genus Dactylogyrus, diplostomatids metacercariae and Rhipidocotyle campanula, parasitic copepodes Ergasilus sieboldi and E. briani) or decreased (myxosporea Myxidium rhodei, cestoda Caryophyllaeides fennica, trematoda Allocreadium isoporum). Differences in the infection rates of fishes in the transect are explained by features of the parasite morphology and biology, and by levels of water contamination.