Life has flourished in the Costa Rican rainforests and marine environments (one in 20 of all plant and animals species may be found in Costa Rica), but there are also over 100 species there on the International Union for the Conservation of Nature and Natural Resources endangered species list. Deforestation, habitat conversion and pollution are the culprits behind many species' attenuation.

Costa Rica has one of the richest populations of bats in the world, consisting of half the mammalian population. Bat species on the list range from the large predatory spectral bat to the Honduran white bat, only about 37 to 47 mm in length, although both are low risk. Felines such as the little spotted cat, Costa Rican cougar and Central American jaguar have been chased from their habitats, and cottontop tamarin, mantled howler and Geoffroy's spider monkey primates have been greatly diminished. Other threatened mammals include the giant anteater, Sambar deer and Baird's tapir.

Costa Rica is home to 894 species of birds, more than in the U.S. and Canada combined. Of these, over 600 are permanent residents, including the threatened bare-necked umbrellabird, black guan and blue-and-gold tanager, but birds like the cerulean warbler and elegant tern are migratory. The Cocos Island finch resides on the Cocos Island 360 miles off the coast of Costa Rica. It is the only one of Darwin's finches not completely endemic to the Galápagos. Other threatened birds include familiar species like the eagle (black solitary eagle), macaw (great green macaw), hummingbird (mangrove hummingbird) and parrot (red-fronted parrotlet).

The five-keeled spiny-tailed iguana and narrow-bridged mud turtle are a few of the reptiles that are endangered, but there are many more threatened amphibians, most of which are frogs or salamanders that are typically represented by great diversity in rainforest environments. The lemur leaf frog and Starrett's treefrog are listed as critically endangered. So are El Empalme worm salamander and two species of toads: the pico blanco toad and pass stubfoot toad. The Monte Verde golden toad has not been seen since 1989 and is considered to be extinct.

Most of the Costa Rican fish on the endangered species list are either near threatened or vulnerable. These include the olive grouper, Pacific seahorse and crown shark. A number of rays are also on the list, such as the bullseye electric ray in the Pacific and the cownose ray in the Atlantic.

There are a number of endangered shadowdamsels, insects that look similar to dragonflies. These include black-backed, elongate, chiriquita, cacao and reventazon species. Many of the other endangered insects are knobtailed dragonflies like the limon, humped, catago, volcano, alajuela and horned species. Two species of freshwater crabs and several marine corals also made the IUCN list.

There are over 9,000 known species of plants in Costa Rica. Endangered plants include members of the legume family such as abarema and the lancepod, the latter of which derives its name from its lance-like fruit. There are also 24 species of the flowering plant eugenia, nine species of the aromatic plant quararibea and two species of the genus virola, which is closely related to the nutmeg and has yellow flowers with a pungent odor. Other major threatened genera include the coralberry, the fan palm cryosophila and the evergreen or dry-season deciduous tree cedrela. The Costa Rican jatropha, manilkara tree and gavilán blanco tree are specifically threatened species of plant.