The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species' genetic diversity. Phylogenetic relationship and phylogeography of 636 individual Tibetan sheep which were collected from the Qinghai-Tibetan Plateau area in China and were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Reference data were obtained from the six reference breed sequences available in GenBank. Phylogeography analysis showed that all four previously defined haplogroups were found in the 15 Tibetan sheep populations but that only one haplogroup was found in Linzhou sheep. Furthermore, clustering analysis divided the 636 individual Tibetan sheep into at least two clusters. The estimated genetic distance and genetic differentiation associate with altitude, suggesting geographic and adaptive effects in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau in China.