The Endangered Species Act of 1973 protects species in danger of extinction. Two classes are recognized: An endangered species is one in danger of extinction throughout all or a significant portion of its range, while a threatened species is one at risk of becoming endangered if measures are not taken to improve its status.

Two species in West Virginia that were once on the federal threatened and endangered species list have recovered sufficiently to be removed from this list. These are the peregrine falcon ("delisted" in 1999), and the bald eagle (2007). These animals are still considered "Species of Greatest Conservation Need" by the West Virginia Division of Natural Resources (DNR). The West Virginia northern flying squirrel was removed from the list in 2008.

Four of the endangered animals in the state are bats. Indiana bats hibernate in several West Virginia caves during the winter, but only a few summer maternity colonies (usually under the loose bark of trees) have been found in the state. Virginia big-eared bats use caves for hibernation and also for rearing their young in the summer. Most of the world's Virginia big-eared bats live in West Virginia. Only two gray bats have been observed in the state, and these bats are considered "accidental" in West Virginia and are not a part of the state's resident fauna. The northern long-eared bat was added to the list in 2022 as White-Nose Syndrome has diminished its population. White-Nose Syndrome is threatening many of the state's cave-dwelling bats. The fungus affects bats while they hibernate, and at some hibernation sites, more than 90 percent of the bats have died due to this condition. White-Nose Syndrome was first observed in West Virginia in 2009.

Another mammal, the eastern cougar, has not been seen in the state since the 19th century. In 2018 the U.S. Fish and Wildlife Service declared it extinct and ordered it removed from the endangered species list.

Freshwater mussels (also called unionids) are an imperiled group of invertebrates. Because these dwellers of stream bottoms cannot tolerate poor water quality, threats are many and include siltation, pollution, and increased water acidity. They are also affected by invasions of non-native zebra mussels, especially in the Ohio River. Eight species of freshwater mussels are listed as federally endangered: pink mucket pearly mussel, clubshell, northern riffleshell, fanshell, James spinymussel, salamander, spectaclecase, and sheepnose. In 2021, the service removed the tuberculed blossom pearly mussel from the list and declared it extinct. The last documented sighting was in 1969 below Kanawha Falls in Fayette County.

Once thought to be extinct, running buffalo clover was rediscovered in West Virginia in 1983. This plant has white blooms and spreads by runners. Shale barren rockcress is adapted to hot, dry south facing shale slopes; its small white flowers are borne on a tall, branching inflorescence. The northeastern bulrush, a rare wetland plant, is found in a few small ponds in Berkeley and Hardy counties while another endangered plant, harperella, is found along four rivers in the Eastern Panhandle; a member of the carrot family, it has small white flowers.

Two species listed as federally endangered are known to exist in West Virginia and nowhere else. The Guyandotte River crayfish has lost 90 percent of its past range and now is found only in two Wyoming County streams. The diamond darter, a type of perch, used to swim in several river basins in West Virginia and Ohio; today, it can be located only in the Mountain State’s Elk River basin. In addition, the candy darter, another freshwater fish, can be found only in the watersheds of the upper Kanawha, Gauley, and New rivers in West Virginia and Virginia.

In January 2024, the U.S. Fish and Wildlife Service ordered the state’s DNR to stop stocking trout in streams known to contain the Candy Darter, Guyandotte River Crayfish, and Big Sandy Crayfish or lose federal funding due to noncompliance with the Endangered Species Act. The streams are Camp Creek in Mercer County, Laurel Creek of Cherry in Greenbrier and Nicholas County, North Fork of Cherry in Greenbrier County, and Pinnacle Creek in Wyoming County.

The Mountain State is home to three species listed as federally threatened. The Cheat Mountain salamander is found only in the higher elevations of five mountainous counties in the state. It is usually associated with red spruce forests. The entire range of the rare flat-spired three-toothed land snail is within the Cheat River Gorge in Monongalia and Preston counties. The Madison Cave isopod is an aquatic subterranean species that occurs in the groundwater under parts of the Shenandoah Valley including portions of Jefferson County. Another threatened species, the Big Sandy crayfish, is known to exist only in McDowell and Mingo counties as well as in two southeast Kentucky counties and three southwest Virginia counties.

Virginia spiraea, a 4-foot high shrub with clusters of white flowers, grows along the banks of high energy streams, with the world’s largest population found along the Gauley River. The small whorled pogonia, a rare orchid with greenish yellow flowers, is found in West Virginia at two sites in Greenbrier County.

Fact sheets on threatened and endangered species are available at the Division of Natural Resources website.