Coral reefs host high densities of large mesopredators that occupy the upper trophic levels of food chains. We used acoustic telemetry to investigate how red bass (Lutjanus bohar) and grey reef sharks (Carcharhinus amblyrhynchos) partitioned habitats within the Rowley Shoals and the Scott Reefs. Areas of 95% kernel utilization distributions (KUDs) of both species overlapped and occurred in habitats near and within channels and the reef front. Some reef sharks remained within the receiver array for many months or years, whereas detections of red bass were more sporadic. Red bass moved over larger areas in March-June, and some disappeared from the array in these months, coinciding with the spawning season of the species. At the Rowley Shoals there was very limited overlap (< 20%) in 50% KUDs of red bass and grey reef sharks, suggesting spatial partitioning in areas of high use. In contrast, there was much greater overlap (> 60%) of 50% KUDs at the Scott Reefs, a difference that may occur as a result of targeted shark fishing at the Scott Reefs. These findings highlight the value of marine protected areas for mesopredators, and emphasize the need for targeted conservation to mitigate effects of anthropogenic pressures like fishing.