The finitude of fossil fuels, concerns for energy security, and the need to respond to climate change has led to growing worldwide interests in biofuels. However, a significant proportion of conventional biofuel feedstocks is produced in the tropics, notably oil palm in Southeast Asia, and soy and sugarcane in Brazil. This is a worrying trend for many tropical biologists, because it is also within the tropics where the majority of the world’s biodiversity hotspots are located (Myers et al. 2000). For at least the next decade, first generation biofuels will still be in demand. In biodiversity hotspots, where a myriad of anthropogenic factors are already driving intense land use conflicts, biofuel production will pose an additional challenge to the preservation of the remaining natural habitats. Here we address the following questions: How does biofuel expansion threaten biodiversity hotspots? How can we reconcile biofuel expansion with biodiversity conservation in these hotspots?