We present a new comprehensive index for mapping the relative conservation value of threatened biodiversity. The index is based on explicit criteria to (1) select threatened species according to regional government responsibility for species’ conservation; (2) combine species’ presence by means of weighting factors based on differences in threat status, sensitivity to disturbance, functional role, and amount of knowledge; and (3) map species distributions at the scale of 1 km×1 km UTM squares or lower from the information available. We tested the performance of the index in the forest of Andalusia (southern Spain), an extensive European region of 87,268 km2, with 43,864 km² (ca. 50%) classified as forest habitats. All species included in the Annexes of the European Birds and Habitats Directives inhabiting the target area, plus the regionally endemic species either ‘Critically Endangered’ or ‘Endangered’ not (yet) covered by the Directives were selected. The final list included 224 species: 81 plants, 76 birds, 31 mammals, 22 arthropods, six reptiles, five amphibians, and three mollusks. Fine-scale distribution maps were available for 108 species (48%). The remaining maps were downscaled from published 10 km×10 km UTM maps using knowledge on species’ habitat requirements and land-use maps. We overlapped the fine-scale maps with the 86,546 forest tiles of the Andalusian Forest Map and weighted presences by a factor of relative conservation estimated for each species to obtain an index of the relative conservation of each forest tile. Index values were higher in protected areas, and in different forest habitats according to expected numbers of endangered species. Index values were correlated with the existence value of threatened species, but the index underestimate existence values especially for the most valuable tiles. The proposed index allows mapping the relative conservation value of threatened biodiversity by integrating knowledge on all threatened species into a single variable. Integration is based on explicit methodological criteria for species selection, combination of relative conservation values, and estimation of downscaled maps. Accurate mapping and synthetic summary of compulsory data on the conservation status of all species present in a territory advise its extended use for threatened biodiversity valuation in both Europe and elsewhere.