The Hawaiian Islands have long been an important laboratory for evolutionary research because their geological histories offer many natural experiments. For example, the Maui Nui complex, 4 islands that have been repeatedly connected and separated by fluctuating sea levels, lie near Hawaii Island, which has never been connected to another island. Here, we examine the genetic consequences of fluctuating island areas and connectivity using microsatellite analysis of 2 widespread, endemic Hawaiian damselflies. We screened 152 Megalagrion xanthomelas individuals from 5 islands at 14 loci and 34 Megalagrion pacificum from 3 islands at 11 loci to explore dispersal patterns and genetic diversity. Our data suggest that Pleistocene fluctuations in sea level alternated between creating land bridges that facilitated gene flow between once and future islands, and ocean channels that inhibited dispersal. Furthermore, interglacial periods of high sea stands likely reduced suitable habitat availability, causing the loss of genetic diversity on Maui Nui due to bottlenecks and founder events. Finally, we propose that gene flow from Molokai to Lanai may be enhanced by assisted dispersal from the trade winds that are channeled between volcanoes on western Maui and eastern Molokai. Our results emphasize the importance of variable microevolutionary processes in Hawaiian biogeography.