Species that are functionally equivalent but with little taxonomical relationship may display similar genetic patterns if the ecological function evolves genetically in the same way. This study investigated the levels of genetic diversity in the D-Loop gene of random samples collected from 21 bat species inhabiting El Ocote Biosphere Reserve (REBISO, for its acronym in Spanish), and whether the genetic diversity pattern could be associated with the ecological role. Genetic differences between functional groups, localities, and species were evaluated through generalized linear models using the Gaussian distribution error family for nucleotide diversity (p) and the Poisson family for haplotype diversity (h) and segregating sites (s). To study the clustering pattern of species based on nucleotide variation, genetic distances (Kimura's two-parameter model) between functional groups were calculated, and a Principal Components Analysis on genetic diversity parameters was run. Most of the species analyzed (20) maintained genetic diversity levels ranging from medium to high in all genetic diversity estimators. According to genetic distances, the species with the same ecological function shared a greater number of nucleotide substitutions, with some exceptions. The Principal Components Analysis did not detect any genetic structure in relation to the ecological function. Our study found no association between the diversity of the D-Loop gene and ecological function; nonetheless, it confirms the importance of REBISO as a reservoir of bat species richness and genetic diversity in Mexico.