Characterization of the species composition of the dominant representatives of Protozoa in natural plague foci is important for the study of certain aspects of ecology and persistence mechanisms of Yersinia pestis. Determination of systematic belonging of amoebas isolated from the soils of the Gorno-Altai high-mountain plague focus in 2016 year was carried out by analyzing nucleotide sequences of ribosomal genes of these protozoans. The analyzed sequences of ribosomal genes were obtained by PCR with specific primers followed by sequencing of PCR products.