The identity and behavior of pollinators are among the main factors that determine the reproductive success and mating system of plants; however, few studies have directly evaluated the relationship between pollinators and the breeding system of the plants they pollinate. It is important to document this relationship because the global decline in pollinators may significantly affect the breeding systems of many animal-pollinated plants, particularly specialized systems. Ceiba pentandra is a tropical tree that has chiropterophilic flowers and a variable breeding system throughout its distribution, ranging from fully self-incompatible, to a mixed system with different degrees of selfing. To determine if regional differences in pollinators may result in regional differences in the outcrossing rate of this species, we used systematic observations of pollinator behavior in two tropical life zones and high-resolution genetic analysis of the breeding system of populations from these two regions using microsatellites. We found a predominantly self-incompatible system in regions with high pollinator visitation, while in environments with low pollinator visitation rates, C. pentandra changed to a mixed mating system with high levels of self-pollination.