Abstract: In order to investigate the origin and differentiation of indigenous goat populations, clarify the genetic background to provide the sound utilization with basic information, partial sequence of mtDNA D-loop of 39 black goats from 3 Chinese and 1 Korean population were sequenced and analyzed. 441 bps sequence was analyzed, 45 polymorphic sites were defined, including 11 singlton polymohic sites and 44 parsimony polymorphic sites, all the 55 sites defined 29 haplotypes, and haplotype diversity is 0.984. Phylogenetic tree defined 3 major lineages, C.aegagrus clustered with lineage A. The relative relationship among populations was also analyzed through pairwise distribution and genetic distance between haplotyoes. The results show that the 4 black goat populations are abundant in genetic diversity, at least have 3 different maternal origins, C.aegagrus is one of the origins of domestic goat.