Sulawesi is an important island for primates. All 17 species that are found there are endemics. The island also includes contact zones between species of macaques (genus Macaca) where hybrids may arise. Sulawesi continues to be deforested, especially in the lowlands most suitable for estate crops and other agricultural products. We carried out an island-wide review of the current extent and rates of deforestation, and the impact this is having on the habitat available to all primates and within macaque hybrid zones. The provinces of West Sulawesi and Southeast Sulawesi suffered the highest rate of deforestation. Macaca ochreata in Southeast Sulawesi and Tarsius pelengensis on Peleng island in Central Sulawesi have lost the most habitat at 14%, followed by M. hecki and M. tonkeana. Forest loss also occurred in all macaque contact zones. The greatest losses occurred at contact zones between the western population of M. tonkeana and M. ochreata. Corn, coffee, cocoa, and oil palm are commodities that are spreading throughout the island. The extent of deforestation in the hybrid zones is alarming, particularly as none of them are represented in protected areas. To help address these problems, a careful integration of conservation and development is suggested, including making trade-offs explicit, and conducting transdisciplinary research on social-ecological systems at the interface of policy and management at local scales.