To reveal phylogeographic features of sable (Martes zibellina) in the southeast part of its range, we analyzed variability of the mitochondrial DNA (mtDNA) cytochrome b gene, tRNA (Pro), tRNA (Thr) and control region (D-loop) sequences from 78 specimens in populations of the Russian Far East, northeast China, and Mongolia. Our results revealed the presence of 49 different haplotypes split into two major phylogenetic groups—clades A and B, the latter separated into two clades, B1 and B2. Comparative analysis of D-loop haplotypes in populations originating from the southeast (Russian Far East, China and Mongolia) and the west (northern Urals) portions of sable range indicated that all three mtDNA clades were present in different regional groups. However, highest diversity of clade B1 in northeast China and its nearly complete absence from the Urals suggest that the southeast sable range, being a refuge during Pleistocene glacial periods, can be considered the center of genetic diversification and possibly origin of this species. All divergence estimates fall within the Pleistocene suggesting that Quarternary glaciations played an important role in phylogeographic differentiation of sable.