Due to its morphological conservatism, the American funnel-eared bats of the genus Natalus have had a complex taxonomic history. In Mexico only one species, N. stramineus, has traditionally been recognized. But recently a new endemic species, N. lanatus, was described in the region as a sympatric sibling species of N. stramineus. Natalus stramineus, with a geographic distribution extending from Mexico to Panama, was subsequently reassigned to N. mexicanus. In this study, we analyzed morphological and molecular characters to determine if two distinct species of funnel-eared bats (N. lanatus and N. mexicanus) occur in Mexico. We found that the proposed diagnostic morphological characters that separate the two taxa are not consistent and rarely differentiate between the two forms. Likewise, phylogenetic analyses do not support the separation of Natalus into two species in Mexico, but there is clearly geographic structure when all Mexican haplotypes are combined. The genetic distance between the haplotypes that could be ascribed to N. lanatus and N. mexicanus was typically within the range of conspecifics and not distinct species. To summarize, the results of both morphological and molecular analyses point to the presence of a single species of Natalus in Mexico.