The snow leopard (Uncia uncia) is a globally endangered and threatened species, and studies on their population and genetic structure has been hampered due to their rugged and remote habitat. Molecular methods incorporating noninvasive sampling of wildlife populations via the collection of scats have provided a new chance for understanding the mysterious snow leopard. In this study a total of 106 scat samples were collected in the dominant distribution areas of Zongjia Township (ZJ) and Nuomuhong Township (NMH) in Dulan County and Suojia Township (SJ) in Zhiduo County, Qinghai Province. DNA was directly extracted from the scats and the mtDNA Cyt b gene fragment was amplified using PCR. 78 scats were successfully amplified and sequenced. Sequences were aligned with the GenBank by BLAST software, and 21 of the scats were identified utilizing DNA as snow leopards (11, 5 and 5 in ZJ, NMH and SJ, respectively. According to the analysis of Clustal W and DNASP software, 4 haplotypes and 7 diversity sites were found in the 21 snow leopard scat DNA, and their haplotype diversity was 0. 384 and nucleotide diversity was 0. 35%. The genetic distance and nucleotide divergence among the 3 snow leopard populations was 0. 002-0. 005 and 0. 200-1. 273, respectively. Therefore, the results showed that the snow leopard has high variation in the mt DNA Cyt b gene and significant genetic distance among the three sampling sites.