The Horn of Africa’s 41 protected areas cover nearly nine percent of the land area, although only about a third of this is in protected areas in IUCN categories I to IV. As in other areas of the African Continent, protected areas vary in their degree of protection and effectiveness across the region. In Oman, the massive 24,785 km² Arabian Oryx Sanctuary is a Natural World Heritage Site famous for the successful reintroduction of the Endangered Arabian oryx (Oryx leucoryx), and Jebel Samhan National Nature Reserve is the home of a population of Arabian leopard (Panthera pardus minor, CR), a Critically Endangered subspecies. Ethiopia has several national parks and sanctuaries, including Awash National Park and Chew Bahir Wildlife Reserve, mainly designed to protect remaining populations of desert-dwelling ungulates. Kenya has the remote Malka Mari National Park in the northeastern corner of the country. Although three protected areas are officially recognized in Somalia, there has been no formal protection of these areas since the breakdown of the federal government in 1991. In Djibouti, the small (100 km²) Forêt de Day National Park is the country’s only reserve.

With such an incomplete protected areas system, current conservation activities in the Horn of Africa are completely inadequate for long-term preservation of its biodiversity. A massive increase in conservation action and targeted funding throughout the region is essential not only in its own right but also to provide the environmental and social sustainability necessary to restore governance through its nations. The only part of the hotspot that is receiving any major international attention is the Socotra Archipelago, which has recently been added to UNESCO’s World Network of Biosphere Reserves. In addition, the United Nations Development Program (UNDP) has begun a major program for "Sustainable Development and Biodiversity Conservation for the People of the Socotra Islands," a five-year program financed with U.S. $5 million from UNDP and the governments of Italy and Yemen specifically to support the people of Socotra through conservation and sustainable use of the islands' unique biodiversity and natural resources.