Located in Dare County, the Alligator River lowlands IBA encompasses the Alligator River National Wildlife Refuge and the embedded Dare County Bombing Ranges. Most of the site is in federal ownership, protected and managed by the United States Fish and Wildlife Service and United States Department of Defense.

The Alligator River Lowlands site is home to a variety of plant and wildlife. Forests include stands of Atlantic white cedar, pond pine, loblolly pine, and cypress-gum swamp. The site is one of North Carolina’s most important sites for the coastal plain population of Black-throated Green Warblers. The creation and management of impoundments has increased waterfowl numbers dramatically in recent years and the refuge now attracts more than 6,000 Tundra Swans and almost 50,000 other waterfowl. Studies of bird migration suggest the site is likely an important stopover for migrating landbirds including wintering sparrows, Eastern Meadowlarks, and Sedge Wrens.

The site was recently named a globally significant site for Northern Bobwhite, and it is one the most significant sites in the state  for Prairie and Prothonotary Warblers.

The United States Fish and Wildlife Service has established several access areas where people can explore the National Wildlife Refuge by canoe or on foot. The majority of the refuge, which includes a vast area of dense pocosin and nonriverine swamp forest, is wild and inaccessible. The refuge is one of a few places in the United States where red wolves have been reintroduced successfully. Anhingas and Red-cockaded Woodpeckers are also found in the refuge in small numbers.