To study the genetic diversity of Chinese indigenous pig breeds, a total of 403 pigs from 10 local populations and 1 exotic Duroc breed were genotyped for 20 microsatellite markers. Heterozygosity and Wright's F-statistics (F(IS), F(ST), and F(IT)) were calculated to determine the genetic variation in those populations. The observed heterozygosities were in the range of 0.31 (Duroc) to 0.66 (Shengxian). The F(IS) value was in a range of -0.07 to 0.48. The mean F(ST) showed that approximately 78% of the genetic variation was within-population and 22% was across the populations. The 10 Chinese local breeds were classified into two major groups according to the phylogenetic tree, which was based on standard genetic distance. Four pig populations, Jianli, Ganxi Two Ends Black, Shaziling, and Dongshan were grouped into one branch. Before the study, these four populations were all classified as Central China Two Ends Black according to coat color, shape of the head, and shape of the ear. The Jinhua pig, which also has the two-ends-black coat color, was also grouped to the same branch but was not traditionally classified into this type. The five populations were located in various provinces in central China. The other five populations, Nanyang Black, Hainan Spotted, Huainan Black, Jiaxing Black, and Shengxian Spotted (black body, white feet), were grouped into another branch. The two groups of pig breeds had the same F(ST) value (0.14) when calculated separately. This value was similar to that of Iberian pigs (0.13) but smaller than that of the European pigs (0.27) as reported by other researchers. Our study showed that large genetic differentiation exists in Chinese pig breeds. The grouping of the five two-ends-black populations into one branch of the phylogenetic tree may indicate that the number of conservation farms can be decreased for this type of pig.