Mysopalacinae (zokors) is a group of fossorial rodents for which the taxonomy has yet to reach consensus. Furthermore, due to their fossorial lifestyle, little is known about their ecology. Molecular data are important to elucidate such aspects. In this paper, the complete mitochondrial DNA genome of Gansu zokor (Eospalax cansus) of the type found in Lintan, China was determined. The genome is 16,354 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes, and two main non-coding regions (the control region and the origin of the light strand replication), the gene composition and order of which are similar to most other mammals. The overall base composition is T 30.0%, C 24.2%, A 33.5%, and G 12.3%, with an A + T bias of 63.5%. These mitogenome sequence data are potentially important for evolutionary, population genetic, and ecological studies of the Mysopalacinae.