Analysis of the 367 mtDNA D-loop sequences (of which 241 sequences were collected from literature) of 399 bp in 13 Chinese domestic donkey breeds revealed 96 different haplotypes with 57 polymorphic sites. The haplotype diversity and the nucleotide diversity were 0.767-0.967 and 0.014-0.032, respectively, indicating abundant genetic diversity in Chinese domestic donkeys. The Neighbor-joining tree of Chinese domestic donkey sequences was constructed with 3 Nubian wild ass sequences, 3 Somali wild ass sequences and 6 Asian wild ass sequences. Our results suggest that the maternal ancestor of Chinese domestic donkeys is highly likely to be Somali and Nubian of African wild ass instead of Asian wild ass.