In this study, we investigated the polymorphisms of STR of Pumi and Lisu minorities with STR genescan marked by fluorescence. Eighty-five alleles of 9 STR in Pumi were detected with the frequency 0.0050-0.5250 and 194 genotypes were found with frequency of 0.0098-0.3235. Sixty three alleles with their frequency of 0.0050-0.4802 and 145 genotypes were found out with frequency of 0.0099-0.3664 in Lisu population. Hi-Square test indicated the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P > 0.05). Statistical analysis showed the followings: H > 0.6 in each locus, the average PIC > 0.7, mean DP > 0.8, EPP > 0.5, indicating the STR markers used in the study were of great value in the researches on minority genetics.