ABSTRACT: Highly migratory species (e.g. sharks, tunas, turtles, cetaceans) present unique conservation management challenges due to their wide-ranging movements. Consequently, the extent to which management areas protect habitats for highly migratory species is often unknown. Within the southeast region of the USA’s exclusive economic zone, highly migratory sharks are target and/or bycatch species in pelagic and bottom longline fisheries. Here, we developed maximum entropy habitat suitability models for great hammerhead sharks Sphyrna mokarran, tiger sharks Galeocerdo cuvier, and bull sharks Carcharhinus leucas within the southeast region based on satellite tag (n = 96) and remotely sensed environmental data. Modeled highly suitable habitats were compared to longline gear management areas to determine what proportion of these habitats are protected from, and vulnerable to, longline fisheries. The percentages of highly suitable habitats overlapping with longline management areas varied by species and season (78% warm, 36% cool season for great hammerhead sharks; 48% warm, 79% cool for tiger sharks; and 2% warm, 100% cool for bull sharks). Highly suitable great hammerhead and tiger shark habitats were relatively well protected from pelagic longline fisheries yet vulnerable to bottom longline fisheries. Additionally, both species were vulnerable to pelagic and bottom longline fisheries off southwestern Florida; thus, extending gear restrictions to this area may benefit both species. Bull shark highly suitable habitats were only well protected from longline gear during the cool season. These results demonstrate how habitat suitability modeling can be used to help assess the efficacy of spatial management strategies and inform conservation plans for highly migratory species.