Far-Eastern grey voles of the genus Alexandromys are a group of 12 species distributed exclusively in the Eastern Palearctic. Morphologically they are hard to be distinguished due to interspecific overlapping of several characters. In recent material of Alexandromys morphometric analyses of teeth (in particular the first lower molar) proved to be a good tool for species identification, although there are overlaps in several measurements. In subfossil and fossil material, preliminary analyses indicated considerable variation in tooth morphology and, in comparison to extant species, the presence of additional morphologically ambiguous forms. In the present study we tested in subfossil and fossil teeth of the genus Alexandromys from Russian Far East whether taxonomic classification based on morphology is in concordance with species determination based on DNA analysis. We also asked whether the morphologically ambiguous forms could be assigned to described species by means of DNA sequence analysis. The material originated from Medvezhyi Klyk Cave Deposits (Primorskyi Krai, Russia) and had an age of 2000–40,000 years. The results showed that the success rate in PCR amplification was ∼50% and it was possible to obtain PCR products of >400bp. The concordance between taxonomic assignment based on morphology and genetics was high. Out of 17 samples that were successful in the sequence analysis, only one yielded a classification that contradicts morphology and one specimen could not be classified since the delivered sequence most probably is a numt (nuclear copy of mitochondrial origin). Although only one of the four unidentified teeth in our sample was successful in the DNA analysis and allowed taxonomic assignment, our results suggest that genetic species determination could be a valuable tool to classify subfossil and fossil teeth in Arvicolinae.