
The Alabama beach mouse (Peromyscus polionotus ammobates) is a federally endangered species which lives along the Alabama coast.

The Alabama cave shrimp is a species of shrimp in the family Atyidae, found only in caves in the state of Alabama.

The Alabama cavefish is a critically endangered species of amblyopsid cavefish found only in underground pools in Key Cave, located in northwestern Alabama, United States in the Key Cave National Wildlife Refuge. It was discovered underneath a colony of gray bats in 1967 by researchers Robert A. Kuehne and John E. Cooper and scientifically described in 1974.

The Alabama sturgeon, Scaphirhynchus suttkusi, is a species of sturgeon native to the United States of America and now only believed to exist in 130 miles (210 km) of the lower Alabama River. The fish has a distinctive yellowish-orange color, grows to a size of about 30 in (76 cm) long and 2 to 3 lb (0.9–1.4 kg), and is believed to have a lifespan of 12 to 20 years. Biologists have known of the fish since the 1950s or 1960s, but the large diversity of aquatic species in Alabama prevented formal identification until 1991.

The boulder darter species of freshwater ray-finned fish, a darter from the subfamily Etheostomatinae, part of the family Percidae, which also contains the perches, ruffes and pikeperches. It is endemic to Alabama and Tennessee in the United States, where it occurs in the Elk River system and Shoal Creek. It is found in small rivers and fast-flowing streams, at least 2 ft (0.6 m) deep, with boulders or a rocky base. It feeds on aquatic insect larvae but little is known of its natural history. The population trend of this fish is unknown but it is affected by a rise in siltation and the impoundment of water within its range by the building of dams. The International Union for Conservation of Nature has assessed its conservation status as being "vulnerable".

The flat pebblesnail is a species of freshwater snail, an aquatic gastropod mollusk in the family Lithoglyphidae.

The flattened musk turtle is a species of turtle in the family Kinosternidae. The species is endemic to the southern United States.

The goldline darter is a small species of freshwater ray-finned fish, a darter from the subfamily Etheostomatinae, part of the family Percidae, which also contains the perches, ruffes and pikeperches. It is found in the United States, primarily in the Cahaba River in central Alabama and the Coosa River in Georgia and Alabama. It is a small fish seldom exceeding 3 in (7.6 cm) in length. It is typically found in areas with moderate to swift currents and a water depth of over 2 ft (60 cm), in the main channels of free-flowing rivers with a rock, cobble or boulder base and aquatic plants. It has been federally listed as a threatened species since April 22, 1992, and the International Union for Conservation of Nature has classified its conservation status as being "vulnerable".

The palezone shiner is a rare species of ray-finned fish in the family Cyprinidae. It is native to Alabama and Kentucky in the United States. It once occurred in Tennessee, but it has been extirpated from the state. There are two populations remaining. It is a federally listed endangered species of the United States.

The plicate rocksnail, scientific name Leptoxis plicata, is a species of freshwater snail with a gill and an operculum, an aquatic gastropod mollusk in the family Pleuroceridae.

Toxolasma cylindrellus, the pale lilliput naiad, pale lilliput pearly mussel, or pale lilliput, is a species of freshwater mussel, an aquatic bivalve mollusk in the family Unionidae, the river mussels. Its host is the Northern studfish

The vermilion darter is a species of freshwater ray-finned fish, a darter from the subfamily Etheostomatinae, part of the family Percidae, which also contains the perches, ruffes and pikeperches. It is endemic to the southern United States, where it only is found in Turkey Creek in Jefferson County, Alabama, part of the Mobile Bay drainage basin. On December 7, 2010, the US Fish and Wildlife Service designated 13 mi (21 km) of Turkey Creek watershed as critical habitat for the darter.

The watercress darter is a species of freshwater ray-finned fish, a darter from the subfamily Etheostomatinae, part of the family Percidae, which also contains the perches, ruffes and pikeperches. It is endemic to the eastern United States where it is only known from the Black Warrior River drainage basin near Birmingham, Alabama.