Abstract: Taking the national key ecological function area-Wuyishan City as the case area, 54 rare and endangered species are selected as indicator species. Based on the assessment of species habitats, the MARXAN model, a systematic conservation planning tool, is used to assess priority areas for biodiversity conservation. The results show that: the total area of the priority areas for biodiversity conservation in Wuyishan is 734.7 km², accounting for 26.1% of the research area, which are concentrated in the northeast, northwest and southeast regions; in the priority conservation areas, the protection ratios of the eight first-level protected species habitats exceed 50% of the total area of their respective habitats. The GAP analysis indicates that there is a spatial mismatch between the priority biodiversity conservation areas and the existing nature reserves. It is recommended to expand and build new nature reserves within the first-level priority area for biodiversity conservation, including the eastward expansion of Wuyishan National Park, the southward expansion of Wuyishan Huanglongyan Provincial Nature Reserve, the newly built forests-wetlands and aquatic wildlife nature reserves in Wutunxi, Dongxi Reservoir and surrounding areas in Wutun Township, the newly built forest nature parks in Shangmei Township and Wufu Township.