Abstract：PCR-SSCP were used to analyzed the mitochondrial DNA(mtDNA) encode region variation of 465 individuals of 9 native goat breeds from 9 provinces and autonomous region in China and 1 foreign breed Angora goat. Accoding to the result of PCR-SSCP,we sequenced the mitochondrial hypervariable region 1 (HVR1) of 118 individuals. The analysis of these sequences reveals the goat breed were classified into four distinct lineages A, B, C and D, The fixation index (Fst =77.77%) suggested that most of the total genetic variation was due to variation within populations,and revealed a weak phylogeographical structure in the goat breeds. Mismatch distribution analysis showed that 2 population expansion happened among goat population.
