The Mountains of Central Asia have long been exploited for grazing, food, timber and fuel. The last few decades, a steady rise in human population (there are about 20 million people in the hotspot) and domestic livestock, and the associated need for land and resources, has made human activity unsustainable in many areas. This has been exacerbated over the last 10-15 years by political and economic changes in the countries of the former Soviet Union. Habitat destruction, overgrazing, and unregulated hunting of animals and collection of plants have emerged as the three major and continuing threats in the hotspot, such that only around 20 percent of the original native habitat remains in pristine condition.
Virtually all of the land in the lowland desert belt and in many foothill areas has been converted to agricultural use. As coal and other fuels have become unavailable and unaffordable, the cutting of trees and shrubs for fuel and building materials has increased. This, together with forest fires, has greatly reduced the area of these habitats, especially in the case of the steppe-shrub communities and the unique and valuable walnut-fruit forests. As an example, between 1995 and 1998, more than 4 500 km² of forest in Kazakhstan were lost due to fires. Expansion of settlements, construction of roads and other infrastructure, recreational facilities, mining and other economic activities have also contributed to habitat destruction and fragmentation.
Many areas have been affected by overgrazing as numbers of domestic livestock throughout the region have increased sharply in recent years. This is particularly the case in the foothills and lower slopes, as well as the alpine and subalpine meadows.
Since the break-up of the former Soviet Union, poaching, especially of larger mammals and birds, has increased sharply. Mountain ungulates are increasingly seen as a source of food, and snow leopard numbers in Kyrgyzstan are estimated to have decreased by 75 percent during the 1990s, as a result of heavy hunting pressure on them and their prey. Falcons are captured and exported to the Middle East, where they fetch a high price from falconers. Unregulated collection of plants also poses a problem to native species; crocuses and tulips have disappeared or become very rare in several areas.
Other threats include the impacts of civil conflict in Tajikistan in the 1990s and the recent war in Afghanistan, as well as the siting of minefields along international borders, which pose a threat to large animals. Damming, reservoir construction and irrigation have disrupted water supplies and drainage systems, and many wetlands have been drained for agriculture. Overfishing and the introduction of alien species further threaten freshwater ecosystems.
Finally, the long-term effects of global warming pose a threat to the environment of the Mountains of Central Asia. It is estimated that glaciers in the area have shrunk by nearly 20 percent in the last 30-35 years, and the long-term destabilizing effects of the melting of frozen upper slopes may lead to the decline or disappearance of many montane taxa in the hotspot.