On the basis of the data of phylogeographical analysis, strains of Yersinia pestis are divided into a number of phylogenetic branches, and in accordance with the traditionally used subspecies classification in the CIS countries, they are divided into five subspecies. We conducted a study of the population structure and genetic characteristics of strains belonging to the phylogenetic branch 0.PE4 and its strains of the Altai subspecies—0.PE4a (Russia, Mongolia), the Hissar subspecies—0.PE4h (Tajikistan), the Talas population—0.PE4t (Kyrgyzstan), and the microtus population—0.PE4m (China). The uniformity of phenotypic and genetic characteristics of strains of the 0.PE4 branch has been established and the necessity of their association into one subspecies, the Central Asian (Y. pestis subsp. central asiatica), has been substantiated. The dendrogram demonstrates the presence of four separate subclusters corresponding to four populations: 0.PE4a (Altai strains), 0.PE4h (Hissar strains), 0.PE4t (Talas strains), and 0.PE4m (microtus strains) in the composition of the 0.PE4 cluster, which we propose to allocate to four biovars of the Central Asian subspecies: Altai, Hissar, Talas, and Microtus. A number of mutations specific only to 0.PE4 strains were detected. A DNA target was found and a method for differentiating the Central Asian subspecies (strains avirulent for humans) from other strains of Y. pestis by Real-Time PCR was developed.