Genetic relationship of 10 indigenous pig populations was analyzed by 10 microsatellite markers. Results showed that different phylogenetic methods led to different results. The NJ phylogenetic tree from Nei's genetic distance was consistent with the facts. The 10 pig populations were divided into 3 clusters. The first cluster was Guizhou miniature pig and its inbreeding lines, Diannan xiaoer and Wuzhishan miniature pig, the second Yimeng black pig and Rongchang pig, and the third Erhualian, Jinhua and Bama miniature pig.