Higher crude‐oil prices, increases in energy imports, concerns about petroleum supplies, and greater recognition of environmental consequences of fossil fuels have spurred a search for alternative sources of fuel. In the aspect of choosing an appropriate source for a long‐term development, it is necessary to decide which is the most sustainable. This article describes a systematic method based on Analytical Hierarchical Process technique to compare biodiesel feedstock alternatives on technical, economical, and sustainable aspects throughout life cycles of biodiesel production. Five biodiesel feedstocks which are jatropha, algae, palm oil, rapeseed, and soybean are taken into consideration in a quantified evaluation. Among these alternatives and with a recommended scoring structure, biodiesel from algae is shown in the calculation results to be the highest ranking substitute for diesel fuel due to its overall better performance in the aspects of environment, economical, safety, raw material performance, and fuel performance. © 2009 American Institute of Chemical Engineers Environ Prog, 2009