Little ground squirrel Spermophilus pygmaeus (Pallas, 1778) is a polytypic species of significant interest for the study of taxonomic diversity, genetic structure, gene flow and genetic diversity. Despite the long history of study, the taxonomy of representatives of the genus Spermophilus in the North Caucasus remains poorly developed. Among the unresolved issues are the phylogenetic relationships between the “mountain” and “plain” ground squirrels of the North Caucasus. An equally important aspect of the work is the study of the genetic diversity of little ground squirrel, given that the species is considered an integral component of steppe and desert ecosystems, providing their most important biocenotic functions. Based on the analysis of the 840 bp mtDNA cytochrome b gene fragment, new data on the genetic variability of S. pygmaeus from the eastern extremity of the Western Caucasus were obtained. Unlike previous studies that showed the so-called mountain ground squirrel to inhabit the Caucasus Mountains, this work identified two haplogroups of S. pygmaeus in the studied areas at an altitude of 1,400–1,700 m above sea level, one of which is close to the lowland (East Caucasian) and the other to the mountain (Central Caucasian) groups of the little ground squirrel. The genetic distance between the two haplogroups was 1.54 %. The different evolutionary ages of the three identified groups of S. pygmaeus in the North Caucasus (A1, A2, and B) are most likely associated with the multi-stage settlement of the studied area by the little ground squirrel. The results of molecular dating suggest that the western haplogroup penetrated as a continuous strip into the Central, Eastern Caucasus and the eastern extremity of the Western Caucasus through the Stavropol Upland and the Caspian Lowland less than 400 thousand years ago. As a result of the first wave of dispersal of the ground squirrel from the Russian Plain, the species became established in the eastern extremity of the Western Caucasus in the area of the village of Khasaut, and in the Eastern Caucasus – in the north of the Nogai Steppe (Sukhokumsk) and in the southern outskirts of the Caspian Lowland (Kar-Kar 1 Valley). The younger age of haplogroup A2 (less than 300 thousand years), also originating from the Eastern Caucasus (Khumtop, Zelenomorsk, Lvovsky 13, Kar-Kar 2), is most likely due to the re-colonization of the Caspian lowland by the ground squirrel, which was regularly flooded by the Caspian Sea in historic times. The absence of a continuous forest belt in the Central Caucasus, in particular in the Kabardino-Balkarian Republic, allowed S. pygmaeus to penetrate into the mountains later, less than 200 thousand years ago, through three gorges: Cherek, Baksan and Malkinsky. It is more likely that the species penetrated into the subalpics of the Western Caucasus (Khurzuk and Uchkulan) from the Central Caucasus, as evidenced by the same evolutionary age of animals of the Western (Uchkulan, Khurzuk) and Central Caucasus. Regarding the taxonomic status of the Caucasian mountain ground squirrel, we consider it premature to draw any conclusions, since not all areas of the Caucasus were covered by research.