By using noninvasive DNA technology,20 fecal samples and 2 muscle samples of Sichuan Snub-nosed Monkeys(Rhinopithecus roxellana)from Baishuijiang Nature Reserve of Gansu province(BSJ),Changqing Nature Reserve of Shaanxi Province(SH) and Shennongjia Nature Reserve of Hubei Province(SNJ) were analyzed and the mitochondrial DNA D-loop fragments were successfully amplified.Sequences were aligned with the GenBank by BLAST software and 22 samples were identified as R.roxellana.According to the analysis by Clustal W and DNASP software,17 haplotypes and 54 diversity sites were found in 22 Sichuan snub-nosed monkey samples with 393 bp length of mtDNA D-loop region.The haplotype diversity was 0.965 and nucleotide diversity was 3.10%.The genetic distance and nucleotide divergence of R.roxellana among BSJ,SH,and SNJ were 0.003-0.098 and 0.08%-2.80%,respectively.Therefore,the results show a high variation in the mitochondrial DNA D-loop region and genetic distance of R.roxellana from the three sampling sites.