DNA samples of 73 strains of Y. pestis ssp. altaica and 65 strains of Y. pestis ssp. pestis isolated in the Gorno-Altaisk and Tuva natural plague areas, respectively, were investigated by the method of VNTR analysis of a (5′-CAAA-3′)n locus. It was demonstrated that strains from the Gorno-Altaisk population of plague microbes possessed genomic polymorphism on the mentioned marker locus, which is reflected in the variability of the size of the amplicon of 250–275 bp, which corresponds to places where the strains were isolated in separate epizootic loci. Conversely, Y. pestis ssp. pestis strains from the Tuva population were conserved by the 5′-CAAA-3′ locus (the amplicon size was 261 bp). During the random sequencing of amplicons, the exact sizes and number of 5′-CAAA-3′ tetranucleotide repeats were determined.