The parasite fauna of fishes of the Murgab river basin (the Bartang, Murgab, Oksu rivers and Lake Sarez) was first investigated. 44 species of helminths, protozoans and crustaceans were recorded from the above area. The ecological analysis of parasite fauna of Schizothorax intermedius, Schizopygopsis stoliczkai and Nemachilus stoliczkai was conducted and the factors affecting its distribution in different parts of the basin and in different species of hosts were established. The data were obtained on the peculiarities of parasitological processes in water bodies investigated.