The geographic range of Alligator mississippiensis (American Alligator) extends to North Carolina, where information on populations is limited. In North Carolina, American Alligators are found near the coast, but typically not on the extensive barrier-island chain known as the Outer Banks. The goal of our study was to determine if habitat varied among sites occupied by American Alligators on islands—the Outer Banks and Roanoke Island—and sites on the adjacent mainland. Water depth, variance in water depth, turbidity, salinity, conductance, and pH varied among sites on Roanoke Island from sites on the mainland (P = 0.008) and the Outer Banks (P = 0.001). However, sites on the mainland and the Outer Banks were similar (P = 0.536). Ultimately, American Alligators may access the Outer Banks and find suitable habitat, but to date, little research has examined American Alligator habitat use in this portion of its geographic range; long-term occupancy is probably limited by of the effects of human disturbance and major storm events.