Pelagic species of dolphins are generally assumed to be nomadic, while coastal/insular species often show strong site fidelity. Rough-toothed dolphins (Steno bredanensis) are characteristically described as pelagic, but studies based on individual identification have shown some level of site fidelity near oceanic islands. Here, we collected photographs for individual identification (n = 108 unique individuals) and biopsy samples (n = 64) to assess genetic diversity, population structure and abundance of rough-toothed dolphins around Moorea and Raiatea (170 km apart) in the Society Islands, French Polynesia. Genotype (14 microsatellite loci) and photo-identification recaptures over two to 12 years indicated long-term site fidelity around Moorea and a high probability of demographic partitioning between Moorea and Raiatea. There was also a marked genetic differentiation between the two islands for both control region mitochondrial haplotypes (450 base pairs, FST = 0.58, p < 0.001) and microsatellite allele frequencies (FST = 0.07, p < 0.001), a pattern confirmed by Bayesian clustering analysis. Around Moorea, estimates of census and current effective population size support a population size in the low hundreds. These results suggest a pattern of small, resident community structure, raising important implications for the management of this species known for depredation issues with local fisheries. Such pattern may be found in other species of pelagic dolphins around oceanic islands, extending the need to conduct similar studies in order to highlight potential conservation issues.