Despite the presence of melon-headed whales in tropical and subtropical waters worldwide, little is known about this species. To assess population structure in Hawai‘i, dedicated field efforts were undertaken from 2000 to 2009. Using only good quality photographs, there were 1,433 unique photo-identified individuals, of which 1,046 were distinctive. Of these, 31.5% were seen more than once. Resighting data combined with social network analyses showed evidence of two populations—a smaller, resident population, seen exclusively off the northwest region of the island of Hawai‘i, and a larger population, seen throughout all the main Hawaiian Islands (hereafter the “main Hawaiian Islands” population). A Bayesian analysis examining the probability of movements of individuals between populations provided a posterior median dispersal rate of 0.0009/yr (95% CI = 0–0.0041), indicating the populations are likely demographically independent. Depth of encounters with the Hawai‘i Island resident population was significantly shallower (median = 381 m) than those with the main Hawaiian Islands population (median = 1,662 m). Resightings of individuals have occurred up to 22 yr apart for the Hawai‘i Island resident population and up to 13 yr apart for the main Hawaiian Islands population, suggesting long-term residency to the islands for both populations.