Vagility, ecological requirements, and forest patches can all influence gene flow among populations. These aspects are critical for the maintenance of genetic diversity in populations. Ectophylla alba is a fruit bat belonging to the family Phyllostomidae with specialized feeding and habitat requirements. Studies examining population genetics in this specialist bat are lacking. In this study, ten microsatellite loci were used to evaluate the current genetic structure of this bat species. Six localities in Costa Rica were evaluated. These localities are included in a landscape with remnants of lowland forests surrounded by cattle pastures, plantations, urban areas, and roads. Our results suggest a genetic population with moderate genetic diversity that was observed at most studied loci, with a statistically non-significant difference between the observed and expected heterozygosity. Most of the genetic variation was observed within rather than among sampled populations. The Mantel test showed a non-significant correlation between genetic diversity and geographic distance. These results suggest that E. alba populations have not shown an effect of habitat fragmentation in the studied area. We argue that the increase of forest patches is too recent to alter genetic diversity among sampled localities. Current migration among populations appears to be high enough to balance allele frequencies among localities.