Most of Hawaii's endemic avifauna are species of conservation concern. Some of Hawaii's endangered waterbirds, however, have increased in number as a result of intensive management of wetlands. To inform these conservation efforts, we examined interisland genetic structure and gene flow within 2 Hawaiian endemic waterbirds, the Hawaiian Coot (Fulica alai) and the Hawaiian subspecies of the Common Gallinule (Gallinula galeata sandvicensis), using microsatellite and mitochondrial loci. Hawaiian Coots and Hawaiian Gallinules occupy coastal wetlands and exhibit similar life history characteristics and generation times, although they may differ in dispersal propensity. Mark–resight data for Hawaiian Coot indicate interisland movements, whereas Hawaiian Gallinules are sedentary. Genetic diversity is partitioned across the landscape differently for Hawaiian Coots and Hawaiian Gallinules; patterns of variation are likely influenced by behavioral and ecological mechanisms. Hawaiian Coots exhibit low levels of structure at microsatellite loci (F_ST = 0.029) and high levels of gene flow among islands. Conversely, Hawaiian Gallinules are highly structured across marker types (microsatellite F_ST = 0.205, mtDNA control region F_ST = 0.370, mtDNA ND2 F_ST = 0.087), with restricted recent gene flow. Patterns of gene flow have changed after the population declines in the early to mid-1900s. Gene flow estimates indicate historical dispersal from Kauai to Oahu in both species, while recent estimates show individual Hawaiian Coots dispersing from Oahu and restricted gene flow between islands for the Hawaiian Gallinule. Changes in gene flow through time suggest that patterns of dispersal may be an artifact of the availability of habitat, which may be indirectly associated with the synergistic influences of population density and wetland quality. Despite recent population size increases for both species, continued threats to Hawaiian waterbirds (i.e. nonnative mammalian predators and invasive plants, avian disease, altered hydrology, and saltwater inundation of freshwater wetlands) will likely require continued active management to maintain viable populations.