Abstract: Variation of goat MSHR gene G676A mutation in 22 populations containing 634 individuals was analyzed. The results indicated that the dominate genotype in the goat populations with white hair were homozygote GG，and the allele G was the superiority gene with a frequency of 0.99. The allele A was the superiority gene with a frequency of 0.33 in red and brown hair goat populations containing 197 individuals, especially up to 0.89 in those of abroad breeds. The frequency of A was 0.21 in 271 goat individuals with black coat color mostly, which was higher than that in the white (0.01) but lower than that in the red and brown (0.33). It could be inferred that genotype AA might be related with red and brown coat color, and GG with white coat color. The results also indicated that the G676A mutation was with higher genetic diversity, but poor in Jianchang Black goat, Leizhou goat, Wuan goat, Duan goat and Jining Grey goat. The genetic differentiation among imported goat populations (0.449) was higher than that among Chinese indigenous goat breeds (0.237), and it was lower between indigenous southern and northern goat populations. The higher gene flow of G676A mutation existed between black hair populations and red and brown hair populations. The clustering of populations based on G676A mutation was basically consistent with the variation of coat and hair color.