The biodiversity in Wallacea varies so much from island to island that nearly every island needs its own protected areas to ensure the long-term conservation of endemic species. This need is particularly urgent in the Moluccas, where there are few protected areas. Only about 24,000 km², seven percent of the original hotspot, is under some form of protection. As an example of the poor representation of biodiversity in the protected areas, only 35 of the 112 Important Bird Areas that have been identified by BirdLife Indonesia are currently protected.
The Wildlife Conservation Society recently carried out a three-year island-wide biodiversity survey on Sulawesi to understand key conservation issues and make recommendations to national, provincial and regional governments. Currently, the most important protected area on the island of Sulawesi is the 3,000-km² Bogani Nani Wartabone Park, which was established in the 1980s as an integrated conservation and development project to protect the forests and the watershed in the area. However, the park is threatened by small-scale gold mining, illegal agricultural encroachment and illegal logging, hunting and rattan collection.
The 2,300-km² Lore Lindu National Park in Central Sulawesi is another important protected area. The Nature Conservancy is working with local government agencies and NGOs to institute training, participatory analysis, awareness raising, and sustainable enterprise programs. In the Togean Islands, Conservation International has been working for nearly a decade with a local foundation on ecotourism development and policy creation with the goal of creating an environmentally sustainable model for regional development and community-based conservation. The local government recently declared its intention to proclaim the Togeans as a marine park for tourism, covering 4,000 km² of marine and terrestrial habitats. The 1,730-km² Komodo National Park includes not only the islands inhabited by Komodo dragons, but also 1,320-km² of coral reefs. Conservation programs there have focused on raising awareness, sustainable fishing techniques, capacity building and the establishment of responsible diving and ecotourism businesses.
BirdLife Indonesia is very active throughout the hotspot, and, together with the World Bank-GEF, promoted a process to resolve community-government conflicts that had prevented progress in forest conservation on the Sangihe-Talaud Islands between northern Sulawesi and the Philippines (with the specific aim of protecting two shrinking forest areas that are the sole home of seven endemic bird species). On Sumba Island in the Lesser Sundas, the work of BirdLife Indonesia and BirdLife International helped lead to the establishment of two national parks to protect the most important remaining forests on the island and promoted community action to stop illegal logging and trapping in the area. BirdLife Indonesia has also undertaken surveys and identified priorities for action throughout the Lesser Sundas and the Moluccas. On Tanimbar Island, in the southeast Moluccas, this has been followed up with a project to help local government and communities plan the management of their still-extensive forests (which are home to eight endemic bird species). On Halmahera, development of conservation action to protect the critical forests on the island was suspended with the violence in 1999 and has been revived in 2004.