The genetic diversity of Wendeng dairy goats, Liaoning cashmere goats, and Anhui white goats, three typical types of Chinese goats (dairy type, cashmere type and leather type), was evaluated using microsatellite markers. Boer goats were chosen as the control. Meanwhile, Beijing goats were tested to analyze their genetic relationship with the aforementioned three types of goats. The results showed that the number of effective alleles (NEA), Nei's unbiased gene diversity (H), and allelic richness (AR) of four Chinese goat breeds were from 5.16 to 6.72, 0.80 to 0.85, and 7.30 to 7.89, respectively, indicating the rich genetic diversity in Chinese goats. However, the results of heterozygote deficit indicated that the inbreeding or artificial selection occurred in Boer and Beijing goats. Genetic differentiation between these breeds was moderate, with a mean FST value of 0.063, similar to some goat breeds in other areas. Phylogenetic tree and principal component analyses indicated that Beijing goats were grouped with Liaoning cashmere goats, then clustered with Anhui white goats, and finally with Wendeng dairy goats. Boer goats, nevertheless, had their own branch. The phylogenetic relationship was consistent with the climatic condition and breeding objective.