Abstract：The genetic diversity of 39 indigenous Chinese goat breeds(Capra hircus) and 1 exotic breed was investigated using 9 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG) through fluorescence PCR. The mean expected heterozygosity across loci within populations ranged from 0.4346 to 0.6951. Genetic differentiation measures were moderate, with a mean FST of 0.115 and GST of 0.112. Percentages of variation among and within populations were 13.3% and 86.7%, respectively. The result of phylogenetic trees (UPGMA) analysis, principal component analysis and Bayesian clustering analyses were similar. Forty goat breeds were divided into 5 clusters. Boer was an individual cluster and the Chinese goat breeds subdivision in 4 clusters, the southwest China cluster, the south China cluster, the central China cluster and the north China cluster. Results indicate that the Chinese goat genetic diversity was rich and the genetic variation existed mainly within breed, and has great potential in breeding.
