The most significant threat facing Sundaland's biodiversity is forest destruction. Most deforestation has occurred in just the last three decades, a result of commercial logging and major agricultural projects in combination with government policies and small-scale agriculture. Some of the threats to the region's forests include rubber production, pulp production, and commercial and illegal logging. In Sumatra, illegal and unsustainable logging and non-timber forest product extraction are widespread, fueled by high demand from China, North America, Europe, and Japan. The military and police are sometimes involved, as are paper industries, which obtain most of their wood from forests rather than plantations. Oil palm plantations are also an increasing threat to forests in the hotspot. Increasing prices for palm oil led the government of Jambi Province, in Sumatra, to plan for the conversion of one million hectares of forest to oil palm; similar development is planned in other parts of Sumatra. Furthermore, the infamous Indonesian Transmigration Program, which moved people from more crowded areas of the country, such as Java, to the less populated islands, has accelerated pressures on biodiversity in some places. Rapid road construction increases the extent and speed of deforestation, by providing access for loggers, settlers, and miners.
Particularly hard hit have been the more accessible lowland forests: recent estimates show that Kalimantan's protected lowland forests declined by 56 percent between 1985 and 2001, primarily from logging, and that less than 33 percent of lowland forest and peat swamp remains across all of Indonesian Borneo. At current deforestation rates, lowland forest in Sumatra and Kalimantan may soon disappear completely. Logging has been extensive in some protected areas; for example, forest loss averaged around two percent per year within Bukit Barisan Selatan National Park between 1985 and 1999, and as much as 9.5 percent per year in Gunung Palung National Park between 1999 and 2002.
In recent years, fires have become a major threat to the forests of Sundaland. Tropical forests do not naturally burn, but logging operations create flammable conditions by leaving fuelwood on the forest floor and by exposing the understory to drying. Fires are also sometimes intentionally lit to convert forests to oil palm plantations. Because few tropical plants are adapted to periodic fires, tropical forests are very slow to regenerate after burning. Under the intense exploitation pressure in the region, these forests may never return. In 1997, 15,000 square km in Sumatra and 30,000 km in Kalimantan were lost to fire.
Today, only around 700,000 km of forest remains, much of it highly fragmented. Only about 100,000 km remains in more or less intact condition, representing approximately seven percent of the original extent of the forest. Most of this remaining primary habitat is montane, and lies in the interior of Borneo and within a few protected areas in Sumatra, Peninsular Malaysia, and the southernmost portion of Thailand. Even these areas are under threat. In Sumatra, protected area management has been severely hampered due political developments in 2001: decentralization has delegated power to 78 local governmental structures, but responsibility for protected areas has remained with the central government, which has little authority or capacity for real enforcement or management.
One of the most insidious threats to the fauna of Sundaland is the wildlife trade. Orang-utan numbers were severely reduced in the past because of the pet trade. Today, tigers and rhinoceroses are the most visible targets of hunting for the Chinese medicine market, for skins, body parts, and horns. Turtles, snakes, geckos, pangolins, bears, and monkeys are exported by the ton from the region on a daily basis. Indonesia has long been the regions leading producer and exporter of snake leather. This trade has been surpassed in recent years by the export of live turtles to East Asia. Most turtle populations throughout the Sundaland hotspot are either in decline or have collapsed. Indonesias massive cage bird trade has also placed a number of species such as Bali Starling and Straw-headed bulbul (Pycnonotus zeylanicus, VU) under serious threat; the latter species, once common across its range, is now confined largely to remote areas.