Identifying areas with relevant features of biodiversity is useful to rank priorities for strengthening the design of well-sited natural protected areas and to optimize resource investment in conservation. This study provides decision makers critical tools for highlighting pieces of land worthy of conservation in Spain. We studied four taxa—amphibians, reptiles, nesting birds and mammals—in a 50 × 50 km grid (n=259 cells). We used five criteria for identifying areas of high-value diversity: species richness, rarity, vulnerability, a combined index of biodiversity, and a Standardized Biodiversity Index that measured all four taxa together. As far as we know, the combined index of biodiversity and the Standardized Biodiversity Index are original. Areas of high-value diversity were defined as those cells within the 15% top segment of ranked values for the different criteria. Congruence of areas of high-value diversity for taxa pairs was moderate to low, and averaged 38.5% for areas of high-value diversity based on the combined index of biodiversity. The performance based on the average proportion of threatened species excluded from areas of high-value diversity followed the rank combined index of biodiversity=rarity (0.3%) > vulnerability (9.9%) > species richness (13.8%). The areas of high-value diversity identified according to the Standardized Biodiversity Index included all amphibian and mammal species, all but one reptile species (categorized as rare) and all but six bird species (three of which were categorized as threatened). About 70% of the areas of high-value diversity identified based on the Standardized Biodiversity Index included natural protected areas. However, they average only 274.6 km2, thus occupying a small fraction of the areas of high-value diversity, and there is no guarantee that the species found in an area of high-value diversity site will be present in its protected fraction. Consequently, we urge managers of natural protected areas to conduct diversity surveys. We also urge that additional natural protected areas be established to include the gap of 30% of areas of high-value diversity not currently protected. We took an step for biodiversity conservation planning in the studied region, and discuss the usefulness of maps of areas of high-value diversity for conservation, ecological restoration, and environmental impact assessment and mitigation.