We used mitochondrial and nuclear genetic markers to investigate population structure of common bottlenose dolphins, Tursiops truncatus, around the main Hawaiian Islands. Though broadly distributed throughout the world's oceans, bottlenose dolphins are known to form small populations in coastal waters. Recent photo-identification data suggest the same is true in Hawaiian waters. We found genetic differentiation among (mtDNA ΦST= 0.014–0.141, microsatellite F’ST= 0.019–0.050) and low dispersal rates between (0.17–5.77 dispersers per generation) the main Hawaiian Island groups. Our results are consistent with movement rates estimated from photo-identification data and suggest that each island group supports a demographically independent population. Inclusion in our analyses of samples collected near Palmyra Atoll provided evidence that the Hawaiian Islands are also occasionally visited by members of a genetically distinct, pelagic population. Two of our samples exhibited evidence of partial ancestry from Indo-Pacific bottlenose dolphins (T. aduncus), a species not known to inhabit the Hawaiian Archipelago. Our findings have important implications for the management of Hawaiian bottlenose dolphins and raise concerns about the vulnerability to human impacts of pelagic species in island ecosystems.