The New Guinea alpine-subalpine zone is the highest, largest, and wettest such region on any tropical island and it preserves great variations in biodiversity between the individual mountain areas. Relatively few plant species are confined to the alpine zone and this may reflect a limited time for adaptation by herbaceous species arriving in the formerly extensive alpine-subalpine biome. In the Pleistocene a zone above 3400 m was affected by glaciation while open subalpine habitat was greatly expanded by cooler climates and low levels of CO₂ which hindered the formation of subalpine forest. With post-glacial warming, the subalpine contracted and open areas were invaded by shrublands and forest. Early to late Holocene opening out of the subalpine forest and shrublands is associated with fire that was a result of hunting by humans. This process starts early in some areas but is late or absent on more remote areas.

The alpine is threatened by increased warming and potential invasion by emergent shrubs but is likely to prove resilient to extinction provided that wet conditions continue to prevail. Changing cultural use of high altitudes suggests that the subalpine shrublands are recovering in some areas. However, some mammals and bird species seem to have been lost or become restricted on mountains that are accessible from population centers at lower altitude. With few exceptions, management consists of benign neglect although widespread fires in 1997–1998 point to continuing human impacts linked to drought events. The large mine on Mount Jaya influences subalpine usage over a large area. Tourism is very minor and unlikely to expand while political problems affect both Papua New Guinea and Papua province and logistics remain a severe difficulty. However, locally managed tourism on Mount Wilhelm provides a good model for future development.