Overall, only about seven percent of the hotspot is under some form of official protection, in nature reserves or other protected areas. Although virtually all of this is in protected areas in IUCN categories I to IV, many reserves are small and isolated and some are not yet fully functioning. Since the break-up of the former Soviet Union, there has been a dramatic decrease in funding, patrols and other management activities in protected areas in this region.
The smallest protected area in the hotspot is the 11 hectare Chinese Walnut Nature Reserve, while Pamir National Park in Tajikistan and the Taxkorgan Nature Reserve in China both cover 15,000 km². Other large protected areas include Issyk-Kul Biosphere Reserve (6,298 km²), in Kyrgyzstan; and Mount Tomur Nature Reserve (1,000 km²) and Boghdad Mountain Biosphere Reserve (1,000 km²), both in the Chinese sector of the Tien Shan. Other notable reserves in the countries of the former Soviet Union include Aksu-Dzhebagly in western Tien Shan, Sary-Chelek in Kyrgyzstan, and Kugitang Strict Nature Reserve in Turkmenistan.
Because international borders often follow mountain ridges, the need for transboundary reserves to protect full mountain ecosystems is increasingly being recognized within the region. Regional cooperation between the countries of the former Soviet Union has increased and a Central Asian Mountain Information Network and a Regional Red List program have been established to coordinate assessments and set up a database of threatened species.
Many international donors are involved in the region, including the Global Environment Facility, whose Western Tien Shan Project supports biodiversity conservation in three counties of western Tien Shan. WWF and Fauna and Flora International are also active in the region. The International Snow Leopard Trust and NABU, a German nature conservation organization, are working on snow leopard conservation in Kyrgyzstan. The governments of Switzerland and Kyrgyzstan are working together to manage remnant walnut forests in Kyrgyzstan, and the University of Berne has set up a program to promote sustainable use of pastures in Central Asia.
Several initiatives in the region are taking a wider approach to issues affecting the environment. A Global Mountain Summit, held in Kyrgyzstan in 2002, explored united approaches for mountain development. The Asian Development Bank and the Swiss government sponsored a Regional Strategy for Sustainable Development of the Mountain Regions of Central Asia. Other programs include awareness raising and education, and ecotourism and trekking initiatives, which, if properly planned, can contribute to the local economy and gain support for conservation.