The genetic diversity and phylogenetic survey of native sheep breeds in the eastern and southern Central Asia were assessed in the present study. The clustering, principal components, structure and F statistics all demonstrate that the native sheep breeds in these regions be classified into two genetic groups: Mongolia-Tibetan sheep group and South-Southeast Asia sheep group. The Mongolia sheep group and the Tibetan sheep group had a certain degree of gene communication from the ancient times. In the present study we demonstrated that the Chinese native sheep populations belonged to Mongolia-Tibetan sheep group. However, the relationships among the sheep populations in Mongolia sheep group in China were not closely related to the geographical distance among sheep populations.