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About eight percent of Maputaland-Pondoland-Albany, or 23,051 km², is under some form of protection, with most of these protected areas in IUCN categories I to IV. Although several of the hotspot's national parks, including the 24,000-hectare Greater Addo Park and the 6,536-hectare Mountain Zebra National Park, are managed by South African National Parks, a statutory body within the Department of Environmental Affairs and Tourism, most protected areas in KwaZulu-Natal fall under the jurisdiction of Ezemvelo KwaZulu-Natal Wildlife. The main conservation areas in southern Mozambique, which include the Licuáti Forest Reserve and the Maputo Elephant Reserve, are managed by the Direcção Nacional de Florestes e Fauna Bravia of the Ministério da Agricultura e Pescas. The 256,644-hectare Greater St. Lucia Wetland Park has been declared a World Heritage Site by UNESCO.
However, law enforcement and protection in conservation areas in Mozambique is poor, and the protected area system in the hotspot is not representative of the biodiversity of the region. This is particularly true in Pondoland, where only a few small conservation areas exist. Grasslands, woody grasslands and coastal forests and thickets are underrepresented in the system. This is in large part due to the fact that most conservation areas have been established with the protection of big game in mind, rather than the preservation of floristically interesting and unique areas.
Current conservation initiatives include efforts to establish a transfrontier protected area linking nature reserves in Swaziland, southern Mozambique and northern KwaZulu-Natal, the establishment of the Baviaanskloof Megareserve and the expansion of the Greater Addo Park and the Mountain Zebra Reserve. The recently completed Subtropical Thicket Ecosystem Planning (STEP) project produced a conservation plan, involving dozens of stakeholders, for the region. The plan identified priority areas for the establishment of new protected areas and raised awareness of the importance of intact thicket ecosystems.
An important private initiative in the region is the conservancy program, which originated in KwaZulu-Natal in 1978, and involves the establishment of committees of landowners who pledge to protect the natural environment or certain natural features, such as a particular species. There are now about 218 conservancies in KwaZulu-Natal alone, covering about 1.5 million hectares.