Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels (Pterodroma sandwichensis) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (δ¹³C, δ¹⁵N and δD, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with Φ_ST = 0.50 (p < 0.0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower δ¹³C and δ¹⁵N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated δ¹⁵N values at the food web base. δ¹⁵N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather δD varied from −69 to 53‰. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies.