Strong hurricanes can cause population reductions in West Indian birds and bats, but the genetic consequences of such reductions have not been documented. For three species of phyllostomid bats, we report on the genetic effects of three strong hurricanes that struck the northern West Indies in 2004. Hurricane Ivan devastated Grand Cayman and severely depressed populations of several bat species. Despite being smaller than pre-hurricane levels, the population of Artibeus jamaicensis (the only species we could resample) on Grand Cayman contained greater mitochondrial haplotype diversity but similar microsatellite allelic diversity compared to pre-Ivan levels. We suggest that hurricane-aided dispersal from Cayman Brac introduced two new haplotypes into the Grand Cayman population. In the Bahamas, two other phyllostomids (Erophylla sezekorni and Macrotus waterhousii) did not suffer population losses or changes in genetic diversity as a result of Hurricanes Frances and Jeanne. Our results suggest that strong hurricanes usually have greater demographic than genetic effects but that hurricane-aided dispersal can occasionally introduce new genotypes or haplotypes into island bat populations.