This paper reports a study on zokors sampled from four localities in alpine meadows in the eastern Qilian Mountains in NW China. We studied the taxonomic status of zokor in small regions by molecular phylogenetic, morphological and habitat features. We sequenced the mitochondrial D-loop sequences, reconstructed phylogenetic trees and estimated genetic distances. In addition, we measured the zokors’ skulls and compared their morphologies. Finally, we investigated the habitat vegetation types, the dominant species of plant, and soil compactness of thezokor habitats. The results showed that the zokors belong to two species，Eospalax cansus and Eospalax baileyi, from four different samples. There were significant differences in orbital width and the tympanic bullae (n_male= 14, n_female = 16,P＜0.05) between the two zokor species, and a significant difference in zygomatic breadth between males of the two zokor species (n_male= 14, P＜0.05). The two zokor species were also obviously different in external characters. E. cansus had spare and short hair on the tail and metapodia. However, E. baileyi had dense hair on the tail and metapodia. E. cansus prefer to live in alpine meadow at lower altitudes.  The dominant plants of its habitat were Kobresia humilis, Potentilla anserina, and Poa annua. E. baileyi prefer to live in higher altitude alpine shrub meadows. The dominant plants of its habitat were Poa annua, Potentilla fruticosa and Elymus dahuricus. There were no differences in soil compaction (P＞0.05) between two zokors’ habitats. This study has provided some technical basis to distinguish E. baileyi and E. baileyi in the field.