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 remove them 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. The West Virginia northern flying squirrel was removed from the list in 2008.

Three 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. White-Nose Syndrome, a condition associated with a newly described fungus, 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, tuberculed blossom pearly mussel, clubshell, northern riffleshell, fanshell, James spinymussel, spectaclecase, and sheepnose. In September 2021, the service proposed removing the tuberculed blossom pearly mussel from the list and declaring it extinct. The last documented sighting was in 1969 below Kanawha Falls.

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 threatened are found in the Mountain State and nowhere else. The Cheat Mountain salamander is found only in the higher elevations of five mountainous counties in the state. This species 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.

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.