Understanding the genetic information of endangered species is very important to conservation and management of wildlife. In this study, we collected scats in Qilianshan National Park (QNP) and Sanjiangyuan National Park (SNP) which are important distribution areas for snow leopard in China. Using a molecular panel that included the mtDNA cytb gene, polymorphic microsatellite loci, we identified snow leopard scat, determined the number of individuals observed, and evaluated genetic diversity. A total of 286 scats were collected and 86 of these were from the snow leopard. Among all scats, 41 individual snow leopard were detected based on unique composite microsatellite genotypes, including 26 in QNP and 15 in SNP. The results indicated that the genetic diversity in QNP and SNP was relatively low based on the numbers of alleles and effective alleles, observed heterozygosity, expected heterozygosity and polymorphism information content. The diversity was higher in QNP than in SNP. Population genetic structure analysis revealed all the snow leopard individuals were divided into 3 genetic clusters and these surveyed populations had moderate levels of differentiation. Two of clusters included individuals from distant areas (QLS and DC) indicating the potential for corridors that link these subpopulations. Our study provides important information on the status and genetic diversity of the endangered snow leopard populations in two critical areas of China.