The Snow Leopard (Panthera uncia) is a globally endangered and threatened species, and studies on them have been hampered due to their unique ecological characteristics and remote habitat. Eight microsatellite DNA loci were used to analyze the genetic diversity and genetic structure of 36 identified snow leopard individuals from three areas including Nangqian (Qinghai), Zhiduo (Qinghai) and Akesai (Gansu). 57 alleles were detected in 8 microsatellite loci, and the mean number of alleles (A) was 7.13. The effective number of alleles (Ne) ranged from 2.190 to 5.488, with uneven Allelic frequency distribution. The expected heterozygosity (He) ranged from 0.543 to 0.847, with an average of 0.759. And the polymorphism information content (PIC) ranged from 0.458 to 0.829, with an average of 0.722. In summary, the selected microsatellite DNA markers were highly polymorphic loci with relatively rich genetic diversity in these snow leopard populations. It is smaller genetic distance of two snow leopards’ groups in Qinghai than those of groups in Qinghai respectively with the group in Akesai (Gansu). The index of Fst (0.053), the index of Nm (4.488) and the result from the Structure software showed that such 3 snow leopards’ groups haven’t been divided and should be viewed as one population.