Due to the combination of general morphological similarity among representatives of particular populations and/or taxa, the taxonomy of the Myotis mystacinus morphogroup is traditionally considered to be one of the most complex topics of bat systematics. We used a combination of genetic and morphological approaches to identify which taxa of the morphogroup inhabit the broader Caucasus region (i.e. the territory between Crimea, Southern Russia, Northern Anatolia, and Northern Iran, incl.) and to define the relationships of these taxa to other Palaearctic populations of the morphogroup. Based on the genetic identification (complete sequence of the cytochrome b gene) of 56 specimens of the morphogroup originating from the region and the subsequent morphological comparison of more than 100 museum specimens, five species were shown to occur in the Caucasus region: Myotis mystacinus s.str., M. davidii, M. alcathoe, M. hyrcanicus, and M. brandtii. While the intraspecific positions of the Caucasian populations of M. mystacinus and M. davidii remain unresolved, the populations of M. brandtii belong to the nominotypical form of this species, and the populations of M. alcathoe represent an endemic subspecies, which is here newly described; M. hyrcanicus is regarded a monotypic species.