The analysis of genetic diversity is routinely used to identify divergent intraspecific units and contribute to the knowledge base of biodiversity. In this study we used mitochondrial genetic diversity to propose three management units (MUs) for the Davy's nakedbacked bat (Pteronotus davyi), an insectivorous forest-dwelling species that is distributed in tropical and subtropical areas of America. We analyzed a 555 bp segment of the mitochondrial DNA (mtDNA) control region in 144 individuals from 18 localities spread across the species distribution range in Mexico. Our results demonstrated that the mitochondrial genetic diversity of P. davyi is distributed in three MUs, namely Gulf North, Pacific-Veracruz and Southeastern, with conservation priority, due to either the high mitochondrial genetic diversity or the high proportion of unique haplotypes, for the following populations: Playa de Oro, Arroyo del Bellaco and Catemaco in the Pacific-Veracruz region, and Agua Blanca, Sardina, Calakmul, Calcehtok and Kantemó from the Southeastern region. The Gulf North unit shows signs of the recent loss of genetic variability. These proposed conservation units could be considered a generalized model of conservation for other species of cave-dwelling bats that share the same habitats.