The Common hamster (Cricetus cricetus) is one of the most endangered mammals in Western and Central Europe. Its genetic diversity in Russia and Kazakhstan was investigated for the first time. The analysis of sequences of an mtDNA control region and cytochrome b gene revealed at least three phylogenetic lineages. Most of the species range (approximately 3 million km2), including central Russia, Crimea, the Ural region, and northern Kazakhstan), is inhabited by a single, well-supported phylogroup, E0. Phylogroup E1, previously reported from southeastern Poland and western Ukraine, was first described from Russia (Bryansk Province). E0 and E1 are sister lineages but both are monophyletic and separated by considerable genetic distance. Hamsters inhabiting Ciscaucasia represent a separate, distant phylogenetic lineage, named “Caucasus”. It is sister to the North phylogroup from Western Europe and the contemporary phylogeography for this species is discussed considering new data. These data enabled us to develop a new hypothesis to propose that in the Late Pleistocene, the continuous range of the Common hamster in the northern Mediterranean extended from the central and southern parts of modern France to the Caucasus; however, its distribution was subsequently interrupted, likely because of climate change.