An integrative analysis of an isolated population of Harting’s vole (Microtus hartingi) from the Eastern Rhodope Mountains (Bulgaria) was carried out by morphological and morphometric methods, computed tomography, Cytb variation data, and experimental hybridization. Substantial changes in the development of the skull and teeth were found. Nevertheless, those voles can live to the senex stage. A phylogenetic reconstruction based on Cytb sequences showed that M. hartingi from the Eastern Rhodopes forms a separate clade, which is a sister clade to the voles from Northeastern Greece (also from the foothills of the Rhodopes). M. hartingi from the Rhodopes is mostly isolated reproductively from M. h. ankaraensis from Anatolia (Turkey), as evidenced by a decrease in the proportion of pairs that started breeding, relatively high mortality of pups, and increased sterility of hybrid males. Possible time of isolation of the Rhodopean population and consequences of the “bottleneck” effect on its current state are discussed. At the same time, we believe that, at present, it is impossible to determine its taxonomic status. It is necessary to recognize M. hartingi from the Bulgarian Rhodopes as an endangered population and to include it in regional Red Lists of Bulgaria.