Natural hybridization between species is not a rare event. In arvicoline rodents, hybridization is known to occur in the wild and/or in captivity. In the Microtus arvalis group, cytogenetic studies revealed that there were two distinct chromosomal forms (2n = 46 but a different fundamental number of autosomes). These forms have been attributed to two cryptic species: the common (arvalis) and Altai (obscurus) voles. Recently, individuals with intermediate karyotypes (F1 and backcrosses) were discovered in central European Russia, and, for this reason, other studies have regarded obscurus and arvalis as conspecific. In the present study, to address the question of the species limits in the Altai vole and to infer its evolutionary history, a phylogeographical analysis combined with multivariate morphometric methods and original chromosome data was performed. Two obscurus lineages were identified: the Sino-Russian and South Caucasian lineages. Both lineages are characterized by low genetic diversity, resulting, in the former, from a past bottleneck event caused by encroaching periglacial areas and, in the latter, from recent rapid population divergence. Introgressive hybridization between the Altai and common voles appears to be the result of a secondary contact following the Last Glacial Maximum in central European Russia. Despite the fact that speciation is an ongoing process in most arvicoline species, the common and Altai voles are genetically divergent, morphologically and karyologically distinct, and exhibit contrasting evolutionary histories. For all these reasons, they should be ranked as species: M. arvalis and M. obscurus.