Abstract On the basis of sufficient plant community survey and quantitative analysis of vegetation environment at Longmenhe region, we seeked the richest area for rare and endangered species using MapInfo Professional 6.0 software firstly. We then applied the GAP analysis methodology to compare the vegetation, the management and the dense distribution area of rare and endangered species status layers. The result shows that the GAPs for planning and management in this area consist of three parts: 1) the area that human interventions are not prohibited in current management practice; 2) the area where developed some natural vegetation types which are not found in current protected area; and 3) the dense distribution area of rare and endangered species that man-made disturbance is not prohibited currently. The area of GAPs is about 1736 hm², accounting for 36.81% of Longmenhe region. Considering biodiversity protection and living standard of local communities, we suggested a number of priority areas for the management of this region.