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A typical representative of Inner Asian Marmotini is the pallid ground squirrel Spermophilus pallidicauda, the intraspecific structure of which has remained unstudied to date. We performed a first study of genetic structure in the pallid ground squirrel, based on variability in the mitochondrial DNA control region and cytochrome b. Besides, we generated ecological niche models to estimate the current and past habitat suitability for S. pallidicauda, in order to assess an influence of paleoclimatic events on the range and genetic structure of this species. Our results revealed two phyletic lineages dividing this species into western and eastern population groups. The divergence of the detected phyla may have resulted from the formation of a climatically induced ecological barrier that separated western and eastern parts of the range in the early Holocene according to our hypotheses about the history of S. pallidicaudarange. The influence of Quaternary climatic changes is a source of intraspecific genetic heterogeneity of faunal components of Asian steppe and semi-desert ecosystems. The detected intraspecific genetic variability of S. pallidicauda, including phyletic lineages which may be considered as Evolutionary Significant Units (ESU), increases the adaptive and conservation potential of the species.