The determination of protected area (PA) boundaries and the level of restrictions is very important for sustainable conservation, and such decisions must involve biodiversity data and assessment. In a PA, the consensus of the government and the locals is crucial to ensure protection-use balance. The PA restrictions constrain legal human activities, and the boundary determination and the restrictions should be based on various scientific analyses to achieve consensus. In this study, a GIS-based approach is proposed to utilize the biodiversity data for efficient conservation and land use planning in Kas-Kekova PA, which is among the most important PAs in Turkey. Spatial analysis methods, i.e., kernel density estimation, natural breaks classification and integrated density index, were performed for the assessment of the habitat networks using georeferenced biodiversity datasets, and the results were evaluated with respect to the actual land use data and the land ownership pattern. The developed spatial analysis approach is efficient to produce the conservation base maps required for regional land use planning, for defining sustainable conservation strategies, and to provide a widely accepted base for land use planning and biodiversity monitoring in the PA; although careful investigations and expert opinions are still required for data deficient areas.