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Genetic diversity is an important component of biodiversity, providing the means for species to evolve and adapt in changing environments. Although regions that retain high genetic diversity provide ideal targets for conservation due to their evolutionary potential, they have been poorly mapped in the Neotropics. Here, we mapped genetic diversity, expressed in this study by nucleotide diversity, for five lizards, four amphibians, and one spider widely distributed in the Brazilian Caatinga, a semiarid vegetation. We identified areas that contain higher genetic diversity, which may be used to establish conservation priorities for the region, and evaluated their representativeness within strict nature reserves. Our results show that only 1.5% of the areas holding higher genetic diversity are within strict nature reserves. However, we show that very high genetic diversity regions are overrepresented inside strict nature reserves and encompass areas such as Brejo Paraibano, Catimbau National Park, and part of the Borborema plateau. Thus, the maintenance of biota's evolutionary potential relies upon the inclusion of areas with higher genetic diversity in future conservation planning.