Islands and insular biotas have been recognized as ideal models for studying adaptive radiations and evolutionary processes. In the present study we investigated the Jamaican fruit-eating bat, Artibeus jamaicensis from Cozumel Island, to evaluate the effect of ecological features on genetic diversity and structure across three different environments, semi-evergreen tropical forest, mangrove, and cenotes, using six microsatellite loci in 105 individuals. Genetic diversity was relatively high (forest H_O = 0.693, H_Nei = 0.825; mangrove H_O = 0.702, H_Nei = 0.710; cenotes H_O = 0.695, H_Nei = 0.847). Pairwise genetic differentiation measures between localities were not significant and the overall level of differentiation was markedly low (F_ST = 0.009, G'_ST = 0.088). Likewise, results showed that A. jamaicensis consists of one genetic group and relatedness among individuals was low. Results are concordant with our predictions that the island population will show high genetic diversity and null structure at the fine spatial scale examined. We conclude that ecological features like dispersal and generalist habits are the factors influencing population structure and genetic diversity of A. jamaicensis on the island, and that factors like the species polygynous mating system, female philopatry and male differential dispersal do not prevail in the island population. Cozumel Island is facing severe conservation problems, mainly from habitat perturbation, urbanization and introduction of exotic species, hence the present genetic information is of great value as a basis for future research and protection of the species.