The terrestrial fauna is much less diverse compared to the marine fauna. There are not many terrestrial animal species, but some are endemic and are important from a conservation point of view. Some mammals are of Asian origin, such as a species of deer (Rusa timorensis) - Javan rusa, wild boars, water buffalo, crab-eating macaques, and civets. Some reptiles and birds are native to Australia, such as the orange-legged scrub, yellow-bellied cockatoo, and helmeted dandelion.
The islands are home to twelve terrestrial snake species, including the Javan spitting cobra (Naja sputatrix), Russell's viper (Daboia russelii), white-lipped pit viper (Trimeresurus albolabris), and Timor python (Python timoriensis). Among the lizards, geckos, limbless lizards (Dibamidae) are found, along with the Komodo warbler. The flower pot toad (Kaloula baleata), the endemic Oreophryne jeffrsoniana and Oreophryne darevskii are found there, as well as the saltwater crocodile (Crocodylus porosus).
There are also goats, cats, and dogs that are feral in the park.
