Although about 12.5 percent of the hotspot is under some form of protection, only about 6.9 percent of the land area is conserved in protected areas that fall within IUCN categories I to IV. This area is inadequate to ensure the survival of the region's diversity.
A number of small, but important, private reserves are found in the hotspot, including the 30km² Bilsa Biological Reserve, which protects one of the last remaining stands of undisturbed forest in this part of Western Ecuador. Although they do not ensure biodiversity conservation, indigenous reserves also serve as an important component of regional conservation and sustainable use. In the Awá Indigenous Reserves straddling the Colombia-Ecuador border, the local people have instituted controls on hunting, an important step towards maintaining the integrity of the forests and preserving ecological processes.
Among the proposed conservation measures for the region is the Chocó-Manabí Conservation Corridor. This corridor, which spans more than 60,000 km² in Colombia and Ecuador, aims to link many of the protected areas in the region, including Katios National Park, Utría and Tatamá National Parks in Colombia, and Machalilla National Park, Mache Chindul Ecological Reserve and Cotacachi-Cayapas Ecological Reserve in Ecuador. The Global Conservation Fund at Conservation International is supporting several initiatives in northwestern Ecuador focused on protecting the remaining intact lowland forests in and around the Cotacachi-Cayapas Ecological Reserve and the Awá Ethnic Reserve.
While it may be possible to set aside large blocks of protected forest in the Colombian and Panamanian portion of the hotspot, the degradation in Ecuador has been too severe. In Ecuador, the survival of some species may depend on reactive conservation operations in the shrinking wet and dry forests. In the critically important dry forests of the Tumbesian Region (southern Ecuador and northern Peru), there is a proposal to establish a transboundary biosphere reserve that would include the Biosphere Reserve of the Northeast, which encompasses three protected areas in Peru, along with the Arenillas Ecological Reserve and several Protected Forests in Ecuador (Puyango, Jatumpamba-Jorupe).
Finally, the vast majority of the Galápagos Islands, which have long been a focus of conservation and investment, is now recognized as both a World Heritage Site and a Biosphere Reserve.
Along with creating additional parks and corridors, the future of conservation in the Tumbes-Chocó-Magdalena hotspot will depend on adequate protection and enforcement to keep existing reserves intact. Lack of management capacity and enforcement has led to severe deforestation in some existing parks, including the Machalilla National Park in southwestern Ecuador and the Los Katios National Park in Colombia. Since January 2002, the Critical Ecosystem Partnership Fund has invested $3.3 million in the Chocó-Manabí portion of the hotspot to fund 24 projects focused on field activities and strengthening local NGO capacity.