Nucleotide variations in the mitochondrial cytochrome b and control region gene sequences were used to investigate genetic differentiations between edge habitats and the interiors of Eospalax baileyi. There were 187 individuals for cytochrome b gene analysis and 155 individuals for control region from 16 populations over the total distribution range. Genetic analysis showed that the habitat edges present a substantial higher genetic diversity than the interiors, which were supported by significant values of haplotypes diversity (t = 69.634, P = 0.009; t = 85.780, P = 0.007) and nucleotide diversity (t = 14.100, P = 0.045; t = 17.146, P = 0.037). Mismatch distribution analyses indicated that there were more stable population pattern in the habitat edges than in the interiors, and that the latter may have undergone a population explosion recently (0.086 to 0.103 million years ago) which may have occurred at the interglacials of the Qinghai-Tibetan Plateau (QTP). These results can be explained by the different extent of disturbances induced by geological events in the QTP. The transition zone between QTP and Loess Plateau colonized by the edges could provide sufficient food and suitable subsistence conditions because of relatively low disturbance. However, the interiors of this species have undergone serious challenges from deep environmental changes.