Abstract: This study analyzed the sequences of mitochondrial DNA D-loop region of partial Chinese native goat breeds (200 individuals in 18 breeds) as well as 25 individuals in 4 introduced goat breeds, combined the completely D-loop sequences that deposited in Genbank from other regions in the world (77 individuals among 15 breeds and 2 wild goat). The results showed that there were 1 212 bp length and 228 mutation sites and 203 haplotypes defined in D-loop region for all the 304 individuals, Haplotype diversity was 0.993±0.001 and Nucleotide diversity was 0.018±0.001, respectively. The Chinese goats were belonging to Clades A and B type while the Pakistan goat contained all the clades (A, B, C and D). It suggested that the Chinese goat breeds had higher genetic diversity and high frequently gene flow among breeds when compared with the Chinese cattle breeds.