The effects of tropical forest fragmentation on frugivorous and nectarivorous bats were studied on recent islands created by the flooding of a dam in French Guiana. Study sites include forest islands isolated by water, and control plots in nearby continuous forest. Studies began 1y before the onset of forest fragmentation and encompassed the first 3y after flooding. Forest fragmentation greatly modified the diversity and abundance of bats. Changes occurred more rapidly in the smallest fragments than in the largest one, and trends were remarkably similar among all the studied islands. Bat captures in islands were characterised by the scarcity of understorey frugivores. Differences in home range size and foraging strategies may explain why understorey fruit bat species are more sensitive to fragmentation than canopy ones. Changes in the frugivorous bat community may have indirect consequences on both the demographic and the genetic structures of plant populations inside forest fragments.