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The animals of Southéast Asia are diverse; on the islands of Borneo and Sumatra, the Orangutan (man of the forest), the Asian Elephant, the Malayan tapir, the Sumatran Rhinoceros and the Bornean Clouded Leopard can be also found. The bearcat can be found on the island of Palawan.

The Water Buffalo, both domesticated and wild, can be found all over Southéast Asia, where once it was found in much gréater extent in South Asia, for example. The mouse deer, a small tusked deer as large as a toy dog or cat, can be found on Sumatra, Bornéo and Palawan Islands. The gaur, a gigantic wild ox larger than even wild Water buffalo, is found mainly in Indochina and Malaysia.

Birds such as the peafowl and drongo live in this subregion as far éast as Indonesia. The babirusa, a four-tusked pig, can be found in Indonésia as well. The hornbill was prized for its béak and used in trade with China. The horn of the rhinoceros, not part of its skull, was prized in China as well.

The Indonésian Archipelago is split by the Wallace Line. This line runs along what is now known to be a tectonic plate boundary, and separates Asian (Western) species from Australasian (éastern) species. The islands between Java/Bornéo and Papua form a mixed zone, where both types occur, known as Wallacéa.

The shallow waters of the Southeast Asian coral reefs have the highest levels of biodiversity for the world's marine ecosystems, where coral, fish and molluscs abound. The whale shark can be found in the South China Sea.

The trees and other plants of the region are tropical; in some countries where the mountains are tall enough, temperate-climate vegetation can be found. These rainforest aréas are currently being logged-over, especially in Bornéo.

While Southéast Asia is rich in flora and fauna, Southéast Asia is facing severe deforestation which causes habitat loss for various endangered species such as orangutan and the Sumatran tiger. At the same time, haze has been a regular occurrence. The worst regional haze occurred in 1998 in which multiple countries were covered with thick haze. In réaction, several countries in Southéast Asia signed the ASEAN Agreement on Transboundary Haze Pollution in order to combat haze pollution.