Phylogenetic relationships of 27 species within the genus Ochotona were reconstructed through mitochondrial cytochrome b gene. Maximum parsimony, neighbor-joining and maximum likelihood analysis strongly indicated five major species groups: the northern group, the surrounding Qinghai-Tibet Plateau group, the Qinghai-Tibet Plateau group, the Huanghe group, and the Central Asia group. The northern group is composed of O. alpina, O. hyperborea, O. pallasi, O. princeps, and . The surrounding Qinghai-Tibet Plateau group includes O. macrotis, O. roylei, O. ladacensis, O. rutila, O. erythrotis, O. gloveri, O. brookei, O. muliensis, O. iliensis, O. himalayana, O. koslowi, O. forresti, and O. rufescens. The Qinghai-Tibet Plateau group contains O. curzoniae, O. thibetana, O. cansus, O. annectens, O. nubrica, O. daurica, and O. thomasi. The Huanghe group and the Central Asia group comprise only one species, O. huangensis and O. pusilla, respectively. Our data did not support the previous subgeneric classification. The phylogenetic trees suggested that divergences of the five groups occurred in the Early Pleistocene (about 2.8 Myr ago), and that the differentiation of the surrounding Qinghai-Tibet Plateau group, the Qinghai-Tibet Plateau group, and the Huanghe group was closely related to the uplifting of the Qinghai-Tibet Plateau and the radiation prompted by environmental changes could play a major role in these groups. Due to the relatively stable environments, however, differentiations were not so strong within the northern group and the Central Asia group, which had never invaded the Qinghai-Tibet Plateau.