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Based on the analysis of a fragment of the cytochrome b (cytb) gene of mitochondrial DNA (mtDNA), the genetic diversity of the little ground squirrel Spermophilus pygmaeus Pallas, 1779 of the Central and Eastern Caucasus was studied. Phylogenetic analysis revealed the existence of two clusters A and B within the western clade of S. pygmaeus 2. Cluster A is formed by haplotypes of ground squirrels from the Eastern Caucasus and the right bank of the river. Volga (Ermakov et al., 2023), and B – only haplotypes of Central Caucasian animals. The distance between clusters A and B reaches 1.3%. The relatively isolated position on the phylogenetic tree of the ground squirrel population of the Central Caucasus, the absence of identical haplotypes in Central and East Caucasian animals, and the distances obtained indicate genetic heterogeneity of the ground squirrel in the North Caucasus. A decrease in haplotypic and nucleotide variability was noted in the Central Caucasian populations of the lesser gopher as compared to those from the Eastern Caucasus, which in general indicates the low viability of S. pygmaeus inhabiting the mountains of the Central Caucasus.