Protected area systems are the cornerstones of government conservation programs in the Indo-Burma hotspot. In total, 236,000 km² is officially protected, representing roughly 10 percent of the original extent of vegetation in the hotspot. However, only 132,000 km² (a little under six percent) is in IUCN protected area categories I to IV. Furthermore, not all forest types and wildlife habitats are adequately represented in this system, including lowland wet evergreen forests, riverine habitats, mangrove forests and teak-dominated deciduous forests.
Collectively, the Lower Mekong countries (Cambodia, Lao P.D.R., Vietnam, and Thailand) have more than 13 percent of their land within a system of protected areas. In 1993, Cambodia established 23 protected areas by Royal Decree; these areas contain over 18 percent of the kingdom's land area. Three forest conservation areas were later established to explicitly promote biodiversity conservation. Lao P.D.R. has 20 protected areas, covering a total of 14 percent percent of the nation's land area. As in Cambodia, most of these protected areas were established in 1993. Vietnam established its protected areas network in 1962, and currently has 95 protected areas. Thailand has the most extensive system of protected areas, with about 22 percent of the nation's land area conserved within 250 protected areas. Formal conservation in the kingdom dates to the 1896 establishment of the Royal Forest Department, but protected areas were only established in the early 1960s.
Elsewhere in the hotspot, Hainan Island contains 26 nature reserves, totaling about 1,190 km², that are managed by the Forestry Department, but there are also a small number of protected areas run by other government departments. Myanmar represents one of the best opportunities for extensive habitat protection in the hotspot, particularly in its relatively large and undisturbed river and floodplain forest systems. A total of 38 protected areas had been declared or officially proposed in Myanmar by 2002.
One way of ensuring that the network of protected areas adequately conserves representative biodiversity is through the protection of species that face the greatest risk of extinction worldwide. Globally threatened species are best protected through targeting conservation investment to the sites in which they occur; these sites are referred to as "key biodiversity areas" (KBAs). KBAs are discrete biological units that contain one or more globally threatened or restricted-range species, and can be managed for conservation as a single unit. In the Indo-Burma Hotspot, the network of Important Bird Areas (IBAs) identified by BirdLife International and partner organizations was used as a starting point, and sites important for other taxonomic groups were then added using data from the published literature, and through consultation with experts. A total of 362 KBAs were defined for Indo-Burma during the first phase of an iterative process; about two-thirds of these sites host threatened or restricted-range birds and mammals. This number should increase as more data becomes available for globally threatened plants and freshwater fish species. Of the sites defined during this initial assessment, only 229 are entirely or partly within protected areas. Thus, many opportunities exist for conservation action outside of protected areas.
In most of the Indo-Burma hotspot, government investment in conservation is relatively limited, with most funding directed towards staff and infrastructure development within protected areas. The exceptions are Hong Kong, India and Thailand. Bilateral donors include Denmark, Japan, the United States, and the Netherlands. Multilateral donors include the World Bank, the Asian Development Bank and the United Nations Development Programme. Several international NGOs are also active in the hotspot; examples include WWF, WCS, FFI, TRAFFIC, CI, and WildAid. On the other hand, corporate investment in conservation is very limited. An exception is the Hong Kong-based Kadoorie Farm and Botanical Garden, which focuses on environmental education, animal rehabilitation and rare plant propagation, and biodiversity surveys in southern China.