Environmental barriers and habitat fragmentation can restrict gene flow, leading to genetic divergence among animal populations. The golden snub-nosed monkey, Rhinopithecus roxellana, is endemic to China, and ranges across 4 provinces. However, over the past 40 years its populations have become fragmented. We investigated the genetic diversity, demographic history and population structure of R. roxellana in 5 reserves in one of its strongholds, the Qinling Mountain forests of Shaanxi. We collected genetic material from 11 monkey bands (a group of individuals containing multiple 1-male units) with a total of 428 samples genotyped at 20 microsatellite loci. Allelic richness and heterozygosity suggested a relatively high level of intra-band genetic diversity. We found no evidence of any genetic bottleneck in these R. roxellana populations. AMOVA and Bayesian cluster analysis revealed that R. roxellana in the 5 reserves are highly structured and form at least 3 distinct subpopulations. These subpopulations concur with major topographical features in the study area, such as mountain ridges, suggesting that dispersal of R. roxellana may be restricted by geographical barriers.