The three Chinese indigenous goat breeds, Anhui white goat (Anbai), Xiangdong black goat (Xiangdong) and Matou, and two imported goat breeds, Boer and Sanen, were selected. The polymorphisms in the 5’ regulatory region and exon 13 of PRKAG3 gene were detected using PCR-RFLP and estimated via heterozygosity and polymorphism information content (PIC). The results showed that four polymorphic loci, C-525A and C-225T in the 5’ regulatory region and T90C and C102T in the exon 13, were found in five goat breeds. The C-525A, C-225T and C102T were low-grade polymorphic loci, but the T90C was moderate polymorphic locus (0.25<PIC<0.50). Of which the heterozygosity in Boer was 0.3750 while that in Xiangdong was 0.2366. The linkage analysis results showed that the average heterozygosities of Anbai (0.2208) and Boer (0.2085) were higher than that of other goat breeds, while that of Matou, Xiangdong and Sanen were from 0.12 to 0.14. From the gene diversity, 5 goat breeds may be divided into three types: Sanen, Boer and Chinese indigenous goat breeds.