New records of Middendorf's vole (Alexandromys middendorffii) in the Russian and Mongolian parts of the Eastern Sayan are reported. Species identification was based on genetic (nucleotide sequence of the cytochrome b) and morphological (configuration of the occlusal surfaces of the M3 and m1 molars) analyses. Middendorf's vole has persisted since the Pleistocene in a small area of the alpine tundra of the Eastern Sayan and Khamar-Daban, and possibly also in the adjacent ridges of the Altai–Sayan and Baikal mountain regions. The discovery of Middendorf's vole near Lake Khuvsgul adds a new species to the list of mammals in Mongolia and simultaneously removes this species from the list of animals endemic to the Russian Federation.