A total of 140 endangered species in Hainan Island were selected as indicator species, and their spatial distribution patterns were analyzed by using mechanism habitat model. Based on the iterative operation with systematic conservation planning tool MARXAN, the priority areas of these species were identified and evaluated. The priority areas had an area of 5383.7 km2, accounting for 15.6% of the total land area of the Island, and mainly distributed in some forest regions (Yinggeling, Jianfengling and Wuzhishan) and in northern part water source regions. In the priority areas, the conservation proportion of 11 1st grade indicator species habitats occupied at least 65% of all the habitats. Through the gap analysis of priority areas and current nature reserves, it was suggested that an expansion of Jianfengling, Yinggeling-Limushan, and Wuzhishan-Diaoluoshan nature reserves and the establishment of Baolonglinchang-Linbiling-Fuwanling protection system should be made, and the protection areas for water source conservation and endangered species should be established in the northern part of the Island.