Giant pandas (Ailuropoda melanoleuca) are now confined to fragmented habitats in western China, with more than 60 % of individuals inhabiting 63 protected areas. Knowledge of the environmental features required by giant pandas is critically important for protected area spatial arrangement and subsequent assessments. Here we developed a distribution model for giant pandas in the Tangjiahe Nature Reserve using Ecological Niche Factor Analysis (ENFA) model. We found that less than 40 % of this key reserve is of high suitability for giant pandas, highly suitable habitat being primarily characterized as coniferous forests away from roads within the reserve. Although there was a clear core zone occupied by giant pandas, which included the vast majority of known giant panda locations, only about 45 % of this zone was classified as highly suitable habitat (suitable and optimal). Therefore, the spatial arrangement within the reserve may need to be modified to effectively manage the remaining population of giant pandas. Of particular concern are several tourism proposals being considered by local government, which, if implemented, will increase the isolation of the local population from those in the surrounding area. Our analysis identifies Caijiaba and Baixiongping as areas that should become conservation priorities. Our approach provides valuable data to advise conservation policy and could be easily replicated across other protected areas.