Spatial prioritization in systematic conservation planning has traditionally been developed for several to many species and/or habitats, and single-species applications are rare. We developed a novel spatial prioritization model based on accurate estimates of remotely-sensed data and maps of threats potentially affecting long-term species persistence. We used this approach to identify priority areas for the conservation of the Endangered Greek meadow viper Vipera graeca, a cold-adapted species inhabiting mountaintops in the Pindos Mountains of Greece and Albania. We transformed the mapped threats into nine variables to estimate conservation value: habitat suitability (climate suitability, habitat size, occupancy, vegetation suitability), climate change (future persistence, potential for altitudinal range shift) and land-use impact (habitat alteration, degradation, disturbance). We applied the Zonation systematic conservation planning tool with these conservation value variables as biodiversity features to rank the areas currently occupied by the species and to identify priority areas where the chances for population persistence are highest. We found that 90% of current habitats will become unsuitable by the 2080s and that conservation actions need to be implemented to avoid extinction as this is already a threatened species with a narrow ecological niche. If threats are appropriately quantified and translated into variables of conservation value, spatial conservation planning tools can successfully identify priority areas for the conservation of single species. Our study demonstrates that spatial prioritization for single umbrella, flagship or keystone species is a promising approach for the conservation of species for which few data are available.