Biodiversity conservation is becoming more challenging and imminent due to rapid habitat loss and fragmentation under ever growing global demand for natural resource. Habitat loss and fragmentation can lower migration rate of a species populations, thereby reducing gene flow and genetic variability, leading to increased risk of extinction. Because of the relationship between genetic diversity and landscape characters, biodiversity conservation research should include study on landscape characteristics and their changes. Thus, conservation efforts should not only focus on a specific species itself, but also consider all components of its habitats. In this paper we discussed the relationship between landscape structure and genetic diversity using the Yunnan snub-nosed monkeys as an example. Landscape genetics is an interdisciplinary of population genetics, landscape ecology, and spatial statistics. It is used to quantify the effects of landscape characters on population genetic structures. Results from such studies may have great applications for biodiversity conservation and reserve management. There are five major research categories: (1) quantifying influence of landscape variables on genetic variation; (2) identifying barriers to gene flow; (3) identifying source-sink dynamics and movement corridors; (4) understanding the spatial and temporal scale of ecological processes; and (5) testing species-specific ecological hypotheses. Landscape genetics is becoming a popular research area, because it opens the possibility to investigate ecological processes through genetic data and to analyze how these processes operate in the real world. Landscape genetics have heuristic, as well as practical, values in encouraging landscape ecologists to think more about biological processes rather than spatial patterns, and in encouraging population geneticists to consider the quality of a landscape instead of mere spatial distance. The use of molecular genetic is a new research method in testing landscape ecological hypotheses. The habitat connectivity was studied using a least-cost model and genetic data of the Yunnan snub-nosed monkeys (Rhinopithecus bieti). We presented the connectivity and the habitat areas that were sensitive to overall connectivity. The Yunnan Snub-nosed Monkeys (Rhinopithecus bieti) is one of the rarest species in severe danger. Due to habitat loss and fragmentation, its gene communication was blocked and genetic diversity was threatened. The results show that only monkey groups in S3 were better connected, and other groups were poorly connected. The subpopulations north to S3 were affected by anthropogenic barriers less than the subpopulations south to S3. The potential dispersal corridor between populations was protracted and the important area to restore was located. The sensitive areas were concentrated in subpopulations among S3,S4 and S5 in central and south areas. These sensitive areas should be protect and restore preferential. Our paper also found that population geneticists could be investigated using landscape ecological data. We proposed that (1) a landscape approach should go beyond testing the effect of distance; (2) disturbance and landscape change could be incorporated into the study design; (3) simulation model might help establish a mechanistic link; (4) the spatial and temporal variability of site conditions was important to explaining quantitative traits and differences. Under the influence of social and economic development, natural ecosystems are increasingly threatened by disturbances such as habitat degradation, climatic changes, and invasive species etc. It is believed that landscape genetics would bridge researchers from micro- to macro-ecology. Our current focus of the research was landscape connectivity using genetic data, but interdisciplinary communication should be encouraged and facilitated for future study.