The effect of landscape on populations is of great importance, especially given the number of species inhabiting patchy landscapes. Developments in geographical information systems are facilitating a greater application of spatial analyses to threatened species, such as the Endangered giant panda Ailuropoda melanoleuca, for which habitat patchiness and quality are key limiting factors. Of all factors that influence the suitability of habitat for the giant panda, topography is not subject to change. Here, we report a spatial and statistical analysis of the high quality topographic habitat preferred by the giant panda across its stronghold in the Qinling Mountains, China. High quality topographic habitat, as indicated by a combination of elevation, slope and aspect, covers 92,788 ha, accounting for 15% of the current range of the species. The distribution of the giant panda closely follows patterns of topography and areas with patches of high quality topographic habitat are strongly associated with areas supporting greater numbers of giant pandas. However, comparisons between our model and the existing reserve system reveals a number of inadequacies. Some of the reserves contain little high quality topographic habitat and many patches of high quality topographic habitat are unprotected. Given the importance of topography and the decisive role it plays in shaping habitat, landscapes containing high quality topographic features must be a critical consideration in the design of reserves for the giant panda. The existing system of nature reserves is heavily weighted towards judicial and administrative boundaries, to the detriment of other factors such as topography.