We used sequence variation within 297 bp of control region mitochondrial DNA (mtDNA) amplified from 53 lesser long-nosed bats, Leptonycteris curasoae (Phyllostomidae: Glossophaginae) captured at 13 locations in south-western United States and Mexico and one site in Venezuela to infer population structure and possible migration routes of this endangered nectar- and fruit-eating species. Phylogenetic analysis using maximum parsimony and UPGMA confirmed species and subspecies distinctions within Leptonycteris and revealed two clades exhibiting 3% sequence divergence within the Mexican subspecies, L. c. yerbabuenae. Even though many roosts contained L. c. yerbabuenae from both clades, weak population structure was detected both by a correlation between genetic differentiation, Fstr and geographical distance and by a cladistic estimate of the number of migration events required to align bat sequences with geographical location on maximum parsimony, as compared to random, trees. Three results suggest that L. c. yerbabuenae are more likely to migrate between sites along the Pacific coast of Mexico or along the foothills of the Sierra Madre Occidental than between these regions. (1) Seventeen of 20 bats which shared an identical sequence were captured up to 1800 km apart but within the same putative migration corridor. (2) Residuals from a regression of Fst on distance were greater between than within these regions. (3) Fewer migration events were required to align bats with these two groups than expected from random assignment. We recommend analysing independent genetic data and monitoring bat visitation to roost sites during migration to confirm these postulated movements.