Habitat connectivity within tropical marine seascapes may be greatly dependent on the movement of large organisms, particularly fishes. Using visual and trap sampling within two small bays in Virgin Islands National Park/Biosphere Reserve, St. John, U.S. Virgin Islands, we documented that large coral reef fishes, particularly large adult grunts, which shelter by day on coral reefs and make nocturnal feeding migrations into seagrass beds, accounted for the greatest biomass and abundance of fishes sampled in seagrass habitat. Using passive tags and sonic telemetry, we documented the nocturnal migration patterns of large adult grunts (bluestriped grunts, Haemulon sciurus), which are similar to the well-documented migration patterns of juvenile grunts. Large grunts showed high site fidelity to nocturnal foraging sites in seagrass beds. Sonic tagged grunts demonstrated little movement in their diurnal shelter sites in the boulder-coral zone, with most individuals making nocturnal migrations into the adjacent seagrass bed. These results provide evidence for strong linkage among adjacent habitats at a small spatial scale and emphasize the importance of inclusion of a diversity of habitats in Marine Protected Areas.