Animal movements, residence times, and subsequently foraging strategies, should vary with habitat quality. We used acoustic and satellite telemetry, as well as stable isotopes, to look at movement patterns, macro-scale habitat use, and trophic ecology of blacktip reef sharks, Carcharhinus melanopterus, between two lagoons (eastern and western) at Palmyra Atoll, a US National Wildlife Refuge in the central Pacific. Sharks in the Palmyra lagoons have relatively small home ranges and appear to obtain most of their energy from the lagoon ecosystem. Sharks showed low levels of migration between lagoons over periods of several years, and individuals in the larger western lagoon tended to have longer residence times than those in the smaller eastern lagoon. Furthermore, for sharks in the western lagoon, there was no relationship between total length (TL) and δ15N, 13C relative isotope concentrations, or a Body Condition index (BC). For sharks in the eastern lagoon, TL was positively related to δ15N and negatively related to δ13C and BC. These results suggest that there are low levels of mixing of sharks between lagoons, and these are leading to differences in trophic ecology and potentially foraging success. Although the causative factors behind these differences are unknown, shark home range location can potentially lead to variation in trophic ecology, even over small spatial scales.