Borneo is the third largest island in the world. In prehistoric times it was connected to the Asian mainland due to geological and climate changes. During the recent ice ages of the Pleistocene and the Holocene separation from the mainland caused extinctions and speciation of fauna on the island.

The Borneo python is a species of non-venomous python endemic to the island of Borneo.

Brilliant rasbora is a species of ray-finned fish in the genus Rasbora. They are found in the Malay Peninsula and in Borneo. Adults can grow up to 5 cm

Chaperina is a genus of frogs in the family Microhylidae. It is the only genus in the subfamily Chaperininae. It is also itself monotypic, being represented by the single species, Chaperina fusca, commonly known as the brown thorny frog, spiny-heeled froglet, and saffron-bellied frog. It is found on the Malay Peninsula, in Borneo and in the Philippines. It is abundant in Borneo but uncommon on the Malay Peninsula and patchily distributed in the Philippines.

The common green frog is a frog species of in the true frog family Ranidae; some sources still use the old name Rana erythraea. It lives in Southeast Asia and is also known as green paddy frog, red-eared frog or leaf frog. The last name, however, commonly refers to the Neotropical tree frogs which make up the subfamily Phyllomedusinae. These are not closely related to H. erythraea, belonging to family Hylidae instead.

Dendrelaphis caudolineatus is a common species of colubrid snake known commonly as the striped bronzeback or bronze tree snake. It is erroneously called 'garter snake' in the Philippines. It is not venomous and it is the most commonly sold snake as a pet. Though in captivity, they don't live as long as in the wild.

The frilled tree frog, rough-armed tree frog, or Southeast Asian tree frog is a species of frog in the family Rhacophoridae found in Brunei, Cambodia, India, Indonesia, Malaysia, Myanmar, the Philippines, Thailand, and Vietnam. Its natural habitats are subtropical or tropical moist lowland forest, subtropical or tropical swamps, subtropical or tropical moist shrubland, rivers, swamps, freshwater marshes, and intermittent freshwater marshes. It is threatened by habitat loss.

The giant river frog is a species of frog in the family Dicroglossidae. It is endemic to Borneo, and found in Brunei, Kalimantan (Indonesia), and Sabah and Sarawak (Malaysia).

The harlequin tree frog is a species of frog in the family Rhacophoridae found in Brunei, Indonesia, Malaysia, Thailand, and the Philippines. Its natural habitats are subtropical or tropical moist lowland forest, subtropical or tropical moist montane forest, freshwater marshes, and intermittent freshwater marshes. It is threatened by habitat loss.
Hose's frog is a true frog species with a wide range in Southeast Asia. This species was named after zoologist Charles Hose.

Hylarana glandulosa, commonly known as the rough-sided frog or the glandular frog, is a species of true frog in the genus Hylarana. It is native to Brunei Darussalam, Indonesia, Malaysia, Singapore, Thailand, and Vietnam. Its natural habitats are subtropical or tropical moist lowland forest, subtropical or tropical swampland, rivers, freshwater marshes, caves, and plantations. It is not considered threatened by the IUCN.

Hylarana signata, commonly known as the striped stream frog, spotted stream frog, or Matang frog, is a species of true frog in the genus Hylarana. It is native to the Malay Peninsula, Sumatra, and Borneo. Its natural habitats are subtropical or tropical moist lowland forests, subtropical or tropical swamps, and rivers. It is not currently considered threatened by the IUCN.

Kuhl's creek frog or large-headed frog is a species of frog in the family Dicroglossidae.
Limnonectes ingeri is a species of frog in the family Dicroglossidae. It is found in Borneo . Its natural habitats are tropical moist lowland forests, rivers, and swamps. It is probably seriously affected by habitat loss, and locally also by collection for food.

Limnonectes palavanensis is a species of frog in the family Dicroglossidae. It is found in the Palawan Island and in Borneo. The species shows paternal care, a relatively rare trait in frogs.
Limnonectes paramacrodon is a species of frog in the family Dicroglossidae. It is found in Malay Peninsula, Borneo, and Natuna Besar. Its natural habitats are lowland swamp forest areas with small rivers and streams. It is becoming rare due to habitat loss.

Malayochela maassi Is a species of cyprinid fish found in Indonesia, Malaysia and Brunei. It is the only member of its genus.

Osteochilus microcephalus is a cyprinid freshwater fish from Southeast Asia.

Osteochilus spilurus is a cyprinid freshwater fish from Southeast Asia. It is found in Thailand, Peninsular Malaysia, Sumatra, Java, and Borneo. It grows to 7.5 cm (3.0 in) SL.
The silver rasbora is a species of ray-finned fish in the genus Rasbora. It occurs in the Mekong, Chao Phraya and Mae Klong basins, Malay Peninsula as well as Borneo, Java and Sumatra.

The smallscale archerfish is a perciform fish of genus Toxotes. As its name suggests, the scales of the smallscale archerfish are smaller than those of other archerfish. They reach a maximum length of 15 centimetres (5.9 in). Smallscale archerfish live in the tropical Indo-Pacific region and are potamodromous, moving between fresh and brackish water through their lifetimes.

Hylarana picturata, also known as the spotted stream frog is a species of frog in the family Ranidae. It is found in Borneo, Sumatra (Indonesia) and possibly the Peninsular Malaysia.

Staurois tuberilinguis is a species in the true frog family (Ranidae). It is widespread on Borneo.

Wallace's flying frog or the Abah River flying frog is a moss frog found at least from the Malay Peninsula into western Indonesia, and is present in Borneo and Sumatra. It is named for the biologist, Alfred R. Wallace, who collected the first specimen to be formally identified.