Biofuels are a new priority in efforts to reduce dependence on fossil fuels; nevertheless, the rapid increase in production of biofuel feedstock may threaten biodiversity. There are general principles that should be used in developing guidelines for certifying biodiversity-friendly biofuels. First, biofuel feedstocks should be grown with environmentally safe and biodiversity-friendly agricultural practices. The sustainability of any biofuel feedstock depends on good growing practices and sound environmental practices throughout the fuel-production life cycle. Second, the ecological footprint of a biofuel, in terms of the land area needed to grow sufficient quantities of the feedstock, should be minimized. The best alternatives appear to be fuels of the future, especially fuels derived from microalgae. Third, biofuels that can sequester carbon or that have a negative or zero carbon balance when viewed over the entire production life cycle should be given high priority. Corn-based ethanol is the worst among the alternatives that are available at present, although this is the biofuel that is most advanced for commercial production in the United States. We urge aggressive pursuit of alternatives to corn as a biofuel feedstock. Conservation biologists can significantly broaden and deepen efforts to develop sustainable fuels by playing active roles in pursuing research on biodiversity-friendly biofuel production practices and by helping define biodiversity-friendly biofuel certification standards.