Indonesia contains one of the world's most remarkable geographical boundaries in its distribution of animals. This dates back to the glacial period when sea level fell all over the world. During this period the islands of Java, Sumatra, Kalimantan and Bali on the Sunda Shelf were joined together with one another and with the Asian mainland, but Irian Jaya, Aru and the Australian continent of the Sahul Shelf were separated. This early geographical separation explains why the tropical animal species of Java, Sumatra and Kalimantan do not exist in Irian Jaya. For the same reason, the kangaroo of Irian Jaya is missing in the other region.

Maluku, Sulawesi and the Lesser Sunda Islands, which lie between the Sunda and Sahul shelves, have a strikingly different fauna. Most of the eastern fauna do not exist in Sulawesi even though this island is close to Kalimantan, being just across the Makassar Strait. Similarly, the animal species of Irian Jaya are not found on Seram and Halmahera, Irian Jaya's closest neighbors. One possible reason for this is that Kalimantan and Sulawesi might have been separated by a deep straight at one point, while the great depth of the Banda Sea kept them apart during the glacial period. Some scientists have attributed the phenomenon to three faunal lines. Alfred Russel Wallace (1823-1913) wrote in his book, "The Malay Archipelago" that Nusantara was separated into an Oriental ecological area (west side) and an Australian ecological area (east side) by a Wallace Line that runs from South to North, passing the Lombok and Makassar Straits and ending in the south eastern part of the Philippines. The Weber line which passes the sea between Maluku and Sulawesi, and the Lydekker line which starts at the edge of the Sahul Shelf Sulawesi Island is in a transition zone known as the Wallace Area. The other two faunal lines are the Weber Line, which passes the sea between Maluku and Sulawesi, and the Lydekker Line, which starts at the Sahul Shelf and skirts the western border of Irian Jaya and the Australian continent. Other scientists, however, prefer to call the area a "subtraction transition zone".

The Directorate General of Forest Protection and Nature Conservation has adopted a national strategy on natural conservation whereby the entire ecosystem is conserved. This is necessary because it is often impossible to preserve wildlife outside its natural habitat. For example, the orangutan, which literally means "jungleman" (Pongo pygmaeus) and only lives in the jungles of Sumatra and Kalimantan, is very dependent on a primary forest habitat. For this purpose, the Directorate General, in cooperation with the World Wide Fund for Nature (W.W.F.), established "orangutan rehabilitation centers" to prepare illegally-captured orangutans for return to life in the wilderness.

The Komodo dragon (Varanus komodoensis), the world's largest lizard, can grow to 3 meters long. Its home is on the Komodo group of reserves, which are comprised of Komodo, Padar and Rinca islands, off the coast of Flores in the eastern part of the country.

The "babi rusa", a deer-like pig (Babyrousa, babirussa), and the 'anoa', a forest-dwelling dwarf buffalo, are among the interesting indigenous animals of Sulawesi. Other indigenous mammals of Sulawesi are the big civet cat called 'musang' (Macrogalidia musshenbroeki); a species of the tersier called 'binatang hantu,' which literally means 'spooky animal' (Torsius spectrum), and several species of the black monkey or 'monyet hitam' (Mococanigra).

Among the vast variety of birds in Sulawesi, the Maleo fowl and the shrubhen are two notable species of the megapode family. Irian Jaya and Maluku are rich in colorful birds, varying from the big and unable-to-fly cassowaries (Casuarius) and the brilliantly-plumaged birds of paradise that belong to the family of Paradiseidoe and Ptilinorhynhidoe and number more than 40 species, to a large variety of birds from the parrot family.

Other members of Indonesia's fauna include the hornbill bird, or rangkonglenggong' of the Bucerotidal family, which is noted for its enormous horn-tipped beak. There are also the Sumatran tiger (Ponthera Tigris Sumatrenesis) and the almost-extinct Java tiger (Ponthera Tigris sondaica). The Mentawai Islands off the west coast of Sumatra are home to the "beruk" a relatively large monkey often trained to pick coconuts; and the 'lutung,' or black monkey, which lives on leaves. The 'Badak Jawa' or one-horned rhino (Rhinoceros sondoicus) lives in Ujung Kulon National Park in West Java, but the smaller badak Sumatra or two-horned rhino (Dicerorhinus sumatrensis) has its habitat in the Mt. Leuser National Park (the largest such park in the country) located around the valley of the Alas river in Aceh, Indonesia's northern-most province. Other notable animals are the "banteng" or wild bull of Java (Bos javanicus); the tree kangaroo (Dorcopsis muelleri) of Irian Jaya; the fresh water dolphin (Orcacelia brevirostris) of the Mahakam river in East Kalimantan' and the proboscis monkey or 'bekantan,' also of Kalimantan.

In addition, there is a great variety of birds, including egrets, herons, kingfishers, hawks, eagles and many others. There are also thousands of species of insects and a large variety of lizards and snakes, Tortoises and turmes, as well as exotic species of fish, crabs, mollusks and other aquatic animals, living both) in salt and fresh water, are also found in great abundance.

Indonesia is known worldwide for her ornamental fish species which are exported to the United States, Japan and Germany. The species most noted for their beautiful colors and shapes include the clownfish (Amphiprion), damselfish (Doscyllus), wrasse (Cori$ gaimardi) and the Coris aygula, which abounds in the Bali Strait. The most common species is the green wrasse (Thalasoma lunare). The butterflyfish (Chaetodontidoe) has a small snout, but longsnouted butterflyfish are also found and include the Forcipiger longirostris and Chelmon rostratus.

Another species, the bannerfish (Heniochus acuminatus) has backfins longer than its body length; and the Moorish idol or Zanclus canescens can measure 20 cm. Angelfish (Pomocanthus imperator), Pomancanthus semicirculatus; Pygoplites-diacanthus, and Auxiphipops navarchus, - Angelfish which belongs to the Pomanconthidae family, are all collected for their beautiful colors.

Surgeonfish (Acanthuridae) and Paracanthurus hepatus are very popular because of their distinguished bluish color. Other beautiful species are the Acanthurus leucosternon, Zebrazoma veliferum and Naso literatus. Living a solitary life is the tiger fish or Balistidae.

Sea horses, or Hippocampus coronatus, of the syngnathidae family are also among the ornamental fish sought. Peacock fish, so named because of their long fins, include the pterois zebra, brachiopterus, volitans, ruselli, miles and radiata varieties. They all belong to the Scorpanidae family. There are many more species of ornamental fish in Indonesia, far too many to mention all.