Birds. The brackish marshes of Cedar Island National Wildlife Refuge and the adjacent open water bodies of Pamlico Sound provide important habitat for waterfowl, wading birds, secretive marsh birds, and colonial waterbirds. The refuge marshes are some of the most important locations for breeding black rails, a species of special management concern in the southeast. They also provide important habitat for seaside sparrows, American black ducks, Virginia rails, and clapper rails. Isolated islands and sand spits are used as breeding sites for American oystercatchers, gull-billed terns, least terns, and other coloni species. The longleaf pine forests may support the federally endangered red-cockaded woodpecker A total of 270 species of birds may be observed at the refuge. Of those, 99 are nesting species. A complete species list is located in Appendix VI. Waterfowl survey results are provided in Table 8.

Mammals. Gray squirrels and marsh rabbits are abundant. White-tailed deer are present, though not in high density. Furbearers that have been observed include raccoon, mink, muskrat, otter, fox, nutria, and opossum. Notable mammals not observed on the refuge, but expected to occur, include bobcat and beaver. A total of 35 mammal species are believed to be present on the refuge, however, no formal inventory has been conducted. A list of species expected to occur in refuge habitats that are typical of the southeastern coastal plain is located in Appendix VI. This list contains 14 species that are primarily carnivorous and 18 rodent species.

Reptiles and Amphibians. A total of 92 amphibian and reptile species are believed to be present on the refuge, however, no formal inventory has been conducted. Species observed include southern leopard frog, green tree frog, black rat snake, eastern cottonmouth, yellow-bellied turtle, and snapping turtle. A list of species expected to occur in refuge habitats that are typical of the southeastern coastal plain is located in Appendix VI. This list contains 42 amphibian and 51 reptile species. The largest group of amphibians is frogs, which include 18 species, followed by salamander/newts, 14 species; toads, 6 species; and other amphibians, 4 species. The largest group of reptiles is snakes, 31 species, of which 3 are venemous, followed by turtles, 11 species; and lizards/skinks, 9 species.