The golden snub-nosed monkey (Rhinopithecus roxellana) is an endemic and extremely endangered species in China. Understanding the population genetic structure of the golden snub-nosed monkey and the key factors affecting, it is very important for the protection of this species. The golden snub-nosed monkey population in the Shennongjia National Nature Reserve is an isolated population in the easternmost part of China. It is reported that out of three populations (Qinglin, Sichuan-Gansu, and Shennongjia), the Shennongjia population is the smallest, and has the lowest genetic diversity. However, studies have shown that this population plays an important role in the genetic evolution of the species. Therefore, protection of the golden snub-nosed monkey in the Shennongjia National Nature Reserve is very important. In this study, genetic structure and genetic diversity of the golden snub-nosed monkey population in the Shennongjia National Nature Reserve were studied using molecular biology techniques and landscape genetics methods. These findings would provide a foundation for the sustainable development of populations and further research on the golden snub-nosed monkey. Twelve selected polymorphic microsatellite loci were used. A total of 455 fecal samples were collected from 11 sites where the monkeys often appear in four main distribution areas in the Shennongjia National Nature Reserve. There were 62 alleles detected, and the number of alleles identified per locus ranged from four to seven. The collected fecal samples belonged to 316 individual golden snub-nosed monkey. The distribution of high-frequency alleles in each locus followed similar trends among different golden snub-nosed monkey groups and study sites; however, the distribution of low-frequency alleles was different. The frequency of alleles less than 0.1 accounted for 21.53%-43.56% in different groups and different sites. The mean observed heterozygosity (H_O), mean expected heterozygosity (H_E), and mean polymorphism information content (PIC) of the population in Shennongjia were 0.626, 0.559, and 0.650; the range of H_O, H_E, and PIC among four groups in the Shennongjia National Nature Reserve were 0.578-0.639, 0.515-0.610, and 0.600-0.641, respectively. Differences in genetic diversity values among groups and sites were not significant. Compared with the Qinglin and Sichuan-Gansu populations, genetic diversity of the Shennongjia golden snub-nosed monkey was low. Nei's genetic distance of four populations ranged from 0.046 to 0.139, and their F_ST value ranged from 0.015 to 0.046. Genetic difference between the Dalongtan and Jinhouling groups was the greatest, and that between the Jinhouling and Qianjiaping groups was the lowest. The isolation-by-distance model showed that the genetic distance at different study sites was not significantly associated with geographic distance. Information from GIS (Geographic Information System) indicates that the main factors influencing the genetic distribution of the golden snub-nosed monkey in the Shenongjia National Nature Reserve were the interference from human activities and their fragmented habitats such as shrubs, grassland and road in the habitat, not their geographical distances.