Habitat fragmentation is a major cause of biodiversity loss; it impedes gene flow between populations and interrupts the network of habitat patches. Populations are faced with a high risk of extinction owing to their small and isolated habitat patches. The maintenance of landscape connectivity can promote population movement between habitat patches, and this is extremely important to maintain gene flow and biological dispersal in fragmented landscapes. Using current habitat patches, the least-cost distance method and graph theory were implemented to study the habitat connectivity across the distribution of the Yunnan snub-nosed monkeys, and the optimal distance threshold of landscape functional connectivity was identified. Priority protected areas referred to as "stepping stones" were quantitatively identified based on highly connected functional components. The least-cost path was estimated to determine restoration priority areas for less connected functional components. This study had the following aims: (1) to explore new methods for identifying the optimal distance threshold, (2) to analyze the connectivity between monkey groups, and (3) to quantitatively analyze priority protected areas among monkey groups. The best resistance assignment for each habitat type was determined by a landscape genetics approach that combines the relationship between the least-cost-distance and gene flow, and reflects the promotion and impediment of the landscape matrix on species movement. The optimal threshold distance of least cost comprehensively reflected landscape features and species distribution characteristics; it incorporated the habitat area of each connected component into the monkey distribution. The priority conservation area was quantified using the landscape index. Based on the results, the optimal threshold distance of least cost was 1400 cost units. Monkey groups were mainly classified into five components that did not exceed this threshold, and the connectivity scores for monkey groups within components was Component 3 > Component 1 > Component 5 > Component 4. "Stepping-stone" patches do not exist in the Longma mountain group, resulting in a disconnect between that group and other monkey groups. This connection should first be restored. The results of this study can facilitate the protection of this and other species.