The goal of this study was to assess the phylogeography of the trumpet nosed-bat (Musonycteris harrisoni) through an analysis of the phylogeographic relationship among populations over its entire distributional range along the Pacific coast of Mexico. We used nucleotide sequence data from the mitochondrial cytochrome-b (≈ 950 bp) and D-loop to assess levels of intraspecific variation in the species. DNA-samples of M. harrisoni were obtained from museums, own field collections and bats provided by other researchers. We analyzed samples collected from 21 different localities. Molecular sequence data were analyzed using neighbour-joining, maximum likelihood and Bayesian studies. Nested clades analyses were used to assess the cladistic arrangement of haplotypes. Across the 21 distinct localities, we found nine haplotypes using cytochrome-b data, and 11 different haplotypes using the D-loop. Nested clade analysis revealed a moderate level of molecular variance among localities. Localities were grouped into two clades, composed of individuals from either the northern or southern portion of the species' range that accounted for 41% of the genetic variance. The northern clade shows little phylogenetic structure and distribution seems to be restricted by the Sierra Madre mountain range. Our results suggest a pattern consistent with the vicariant allopatric divergence/speciation model, influenced by habitat loss and fragmentation.