Sichuan snub-nosed monkey (Rhinopithecus roxellanae) is an unique primates in china, witch is in severe danger now and is mainly distributed in Shanxi，Hubei, Sichuan and Gansu province. In recent years, since the forest has been cut excessively and human activities have become increasingly frequent, habitat loss and habitat fragmentation have caused the population isolation and differentiation, the reduction of genetic diversity in Sichuan snub-nosed monkey. Hubei Shennongjia National Nature Reserve is one of the major habitating areas for Sichuan snub-nosed monkey in China. In order to understand the genetic structure of the species for effective conservation, a total of 126 samples were collected from two natural populations in the reserved region, including 60 fecal samples from Dalongtan population, and 63 fecal samples plus 3 muscle samples from Qianjiaping population. The genetic structure and diversity of the populations were estimated by analyzing the samples for mitochondrial DNA (mtDNA) gene fragment, and 9 selected microsatellite loci including D6S474, D3S1768, D1S533, D8S505, D15S644, D1S207, D7S1830, D17S1290, D5S820 In addition, sex identification of the samples was performed using Y chromosome-markers. The results of analysis showed that: (1) a total of 20 haplotypes and 27 diversity sites were found in the 24 random samples at a 401 bp region of mtDNA D-loop, with haplotype diversity value equals to 0982, and nucleotide diversity was 00129. (2) All of 9 microsatellite loci were stably detected in 117 of total fecal DNA preparations and genotyping success rate was 87%, two loci showed deviation from Hardy-Weinberg equilibrium. The average effective number of alleles was 3.85, the average observed heterozygosis and polymorphism information content were 0745 and 0595, respectively. By using Y chromosome marker techniques, 18 male and 40 female was identified in 58 unique Sichuan snub-nosed monkey genotypes. This sex identification technique is very simple, reliable, and especially applicable for the fecal DNA test. These results indicated a high level of genetic diversity in Sichuan snub-nosed monkey in Shennongjia National Nature Reserve. All the same time, the two populations we have invested showed a significant genetic differentiation. Some protection advices were proposed for the species-source saving and population rejuvenation of Sichuan snub-nosed monkey according to protection genetics and research achievement above.