Twenty years ago, Indonesia used the best principles of conservation biology to plan a national protected area system based on representativeness, irreplaceability, complementarity, and connectivity. Large areas of all habitats were proposed as conservation areas within each biogeographic region. Subsequently, all of the country’s forests (more than 70% of the total land area) were allocated for production, watershed protection, or conservation, and Indonesia endorsed the principles of sustainable forest management. Unfortunately, these scientific principles were never fully reconciled with national policy and practice, even though Indonesia was one of the first signatories to the Convention on Biological Diversity. Today, Indonesia is a society in transition, torn apart by economic and political crises, and the gap between scientific best practice and the reality of current forest mismanagement could hardly be wider. If the current state of resource anarchy continues, the lowland forests of the Sunda Shelf, the richest forests on Earth, will be totally destroyed by 2005 on Sumatra and 2010 on Kalimantan. Where did things go wrong?