The transitional nature of the biota has resulted in the presence of many mammals from Asia and several reptiles and birds from the Australasian bio-region. Compared with the rich marine life the terrestrial fauna is small. The Park is best known for the Komodo monitor Varanus komodoensis (VU), the world’s largest lizard, which can grow to 3m long. The population on Komodo island, was estimated in 2001 by a team from the Zoological Society of San Diego, at 2259 individuals. An earlier estimate of about 5.700 was said to be distributed over the islands of Komodo (2,900), Rinca (900), Gili Motong (<100) and in coastal regions of western and northern Flores.The species was last seen on Padar in 1975 (Kvalvagnaes & Halim,1979). Its favoured habitat is tropical deciduous forest, and, to a lesser extent, open savannah. It is carnivorous, eating occasional large meals when it eats all of its prey, and is well adapted to living without water (Auffenburg, 1981). The rest of the herpetofauna is rich, with 12 land snakes including the common cobra Naja naja sputatrix in disturbed land, Russel’s pit viper Vipera russelli and green tree viper Trimeresurus albolabris, 9 species of skink Scincidae, geckoes Gekkonidae, limbless lizards Dibamidae and monitor lizards. There are several amphibian species in the cloud forest: Sphenomorphus schlegeli, S. striolatus and the frog Oreophryne jeffersoniana. Savannah species include Emoia similis, and Asian bullfrog Kaloula baleata. Tropical deciduous forest supports reptiles such as Sphenomorphus florensis, Trimeresurus albolabris, Dendrelaphis pictus and Lycodon aulicus. (Auffenburg, 1980).
The mammalian fauna is characteristic of the Wallacean zoogeographic zone, with relatively few terrestrial species, including several bats, the endemic Komodo rat Komodomys rintjanus (VU), crab-eating macaque Macaca fascicularis and palm civet Paradoxurus hermaphroditus lehmanni. Introduced species, such as the Timor deer Cervus timorensis, the main prey of the lizard, and wild boar Sus scrofa, as well as feral domestic animals including horses and water buffalo Bubalis bubalis, form important prey species for the Komodo monitor. Some 72 species of birds have been recorded, including yellow-crested cockatoo Cacatua sulphurea (CR), noisy friar bird Philemon buceroides and dusky and orange-footed scrub fowl Megapodius freycinet and M. reinwardti.
Indonesia is unique in that marine flora and fauna from both Indian and Pacific oceans intermingle through gaps in the island chain. In fact the local straits are on a migration route for whales. In the Park the marine zone covers 60% of the area and its biodiversity is very high. It has a wide variety of depths and bottom conditions and the upwelling of nutrient-rich water from deeper areas of the archipelago results in a rich reef ecosystem. The marine life includes foraminifera, cnidara, ascidians, worms, crustaceans, molluscs, cartilaginous and bony fishes, marine reptiles, and mammals including 16 species of cetaceans, ten species of dolphin, sharks, manta rays, dugong Dugong dugon (VU) and five species of turtle. These include blue whale Balaenoptera musculus (EN), fin whale B. physalis (EN), humpback whale Megaptera novaeangliae (VU) and sperm whale Physeter catodon (VU), also leatherback turtle Dermochelys coriacea (CR), hawksbill turtle Eretmochelys imbricata (CR), olive ridley turtle Lepidochelys olivacea (EN) and green turtle Chelonia mydas (VU). Species of high commercial value are sea cucumbers, Holothuria, Napoleon wrasse Cheilinus undulatus, and groupers (Mous, 2002; PHKA, 2004).
The coral reefs were once rich, but only isolated patches of reef now remain owing to anthropogenic disturbance (Kvalvagnaes & Halim, 1979). In 1998 185 sites were sampled by TNC and the live reef coverage found was 19%. These habitats harbor more than 1,000 species of fish, 200 species of reef-building coral, and 70 species of sponge (Mous, 2002). The dominant corals on most reefs are species of Acropora, particularly the tabular coral Acropora symmetrica, Millepora and Porites. Fungia spp. are present on reef slopes. In areas of strong currents, the reef substrate consists of an avalanche of coral fragments, with only encrusting or low branching species, such as Seriatopora caliendrum and Stylophora pistillata being able to withstand the rapid water flow. More protected reef slopes, for example in Slawi Bay, are dominated by species of the genera Heteropsammia and Heterocyathus. Reefs off the north-east of Komodo have a high diversity of species including branching Acropora, Hydnophora, Seriatopora and Caulastrea, as well as massive Porites, plate-like Echinophyllia, Merulina, Pachyseris and numerous Fungiidae. The reefs off Gili Lawa Laut are variable, ranging from the sheltered southern bay with its large stands of Pachyseris, Echinopora, Mycedium, Echinophyllia and Montipora, interspersed with thickets of Acropora, to the more exposed northern reefs which have a spur and groove structure dominated by Porites. Seriatopora and Acropora (UNEP/IUCN, 1988).