Sturnira parvidens and Sturnira hondurensis are two frugivorous bat species distributed throughout the Mesoamerican region. Sturnira parvidens inhabits tropical lowland forests and S. hondurensis montane cloud forests. Their populations are respectively separated by the intervening highlands or lowlands. We used mitochondrial DNA control region sequences to compare genetic structure among the populations of these two species in the region of the Gulf of Mexico. We also measured genetic connectivity among their populations and assessed the distribution model for each species. We found high genetic diversity in both species: the F_ST comparisons values were low to high in S. hondurensis and low in S. parvidens. For S. hondurensis, we found isolation by landscape resistance (IBR) where the highland habitat heterogeneity may have restricted gene flow among the populations of the Sierra Madre Oriental, Sierra de Los Tuxtlas, Chiapas and Guatemala. For S. parvidens, the isolation is explained by geographic distance rather than by landscape heterogeneity.