To elucidate the evolutionary history of snow voles, genus Chionomys, we studied the phylogeography of Chionomys nivalis across its range and investigated its relationships with two congeneric species, C. gud and C. roberti, using independent molecular markers. Analyses were based on mitochondrial (~940 bp cyt b) and Y-chromosomal (~2020 bp from three introns) genetic variation. Our data provide conclusive evidence for a Caucasian and Middle Eastern origin for the three species and a subsequent westward expansion of C. nivalis. In addition, we discuss the taxonomic status of the genus Chionomys in relation to the genus Microtus.