Habitat fragmentation is thought to lower the viability of tropical trees by disrupting their mutualisms with native pollinators. However, in this study, Dinizia excelsa (Fabaceae), a canopy-emergent tree, was found to thrive in Amazonian pastures and forest fragments even in the absence of native pollinators. Canopy observations indicated that African honeybees (Apis mellifera scutellata) were the predominant floral visitors in fragmented habitats and replaced native insects in isolated pasture trees. Trees in habitat fragments produced, on average, over three times as many seeds as trees in continuous forest, and microsatellite assays of seed arrays showed that genetic diversity was maintained across habitats. A paternity analysis further revealed gene flow over as much as 3.2 km of pasture, the most distant pollination precisely recorded for any plant species. Usually considered only as dangerous exotics, African honeybees have become important pollinators in degraded tropical forests, and may alter the genetic structure of remnant populations through frequent long-distance gene flow.