For the first time all members of Sicista caucasica species complex were genotyped using one mitochondrial and five nuclear markers. We revealed that there are two lineages in the group: western (caucasica + klucorica) and south-eastern (armenica + kazbegica). This phylogeographic pattern corresponds with recent findings on several other species of small mammals of the Caucasus (moles, snow voles, dormice). An unexpectedly high hidden diversity is found within kazbegica and kluchorica. Also, we confirmed the presence of highly divergent cryptic species in S. tianschanica. The results of the molecular clock analysis suggest that the S. caucasica group separated from its sister taxon - the S. betulina-subtilis group - in the Late Pliocene. Major division within the S. caucasica group occurred in the Upper Early Pleistocene (~ 1.16 Mya). The split in the south-eastern lineage leading to modern S. kazbegica and S. armenica should have happened at ~ 1 Mya; the division of the western lineage took place in the Middle Pleistocene (~ 570 Kya). The approximate ages for the basal splits in S. kazbegica and S. kluchorica are estimated at 230 Kya and 350 Kya, respectively.