Abstract The origin of Chinese sheep is unclear yet. There is a large controversy between the Dual Origins and the Three Origins. For the further study on the origin and genetic diversty of sheep, the complete sequences of mitochondrial DNA(mtDNA) D-loop of 133 individuals in 10 Chinese sheep (Ovis areis) breeds were determined with primer pairs which were designed by Primier Premier 5.0 based on the sheep mitochondrial genome sequence. And the results were analyzed by the Laser Gene, MEGA4, Clustalx1.83 and other software. The results showed that the length of whole mtDNA D-loop of Chinese sheep was 1 106~1 182 bp. There were 103 different haplotypes and 155 polymorphic sites. The results indicated that Chinese domestic sheeps had abundant genetic diversity. The NJ tree results indicated that there were two main branches in Chinese domestic sheeps, O. musimon formed one of the branchs, while O. vignei and O. ammon was clustered together, which indicated that O. musimon had more contribution to Chinese domestic sheep breeds. Ten Chinese domesticated sheep species measured in this study were divided into two branches A and B, which indicated that there were at least two maternal origins and the Asia-A was the main haplotype.From the species level, this study evaluated the genetic diversity of domesticated sheep in China. It is pointed out that the Chinese sheep is divided into two branches, and a theoretical basis is provided for the establishment of the domesticated sheep populations relations in China and the protection of germplasm resources
