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Studies have shown that the magnitude of pollutant emissions (e.g., NO and PM) from diesel engines operating on fatty acid methyl esters (i.e., FAME biodiesel) are related to the fatty acid composition of the triglycerides present in the bio feedstock. Specifically, NO emissions have been shown to increase with increasing levels of unsaturation in the hydrocarbon chain and decrease with increasing carbon chain length; and PM emissions have been shown to decrease with increasing carbon chain length. Little work has been done to date to characterize the pollutant emissions of algae-based FAME, which have far different fatty acid composition than FAME derived from typical vegetable or animal fat feedstocks. Accordingly, the goal of the present study was to characterize the performance and emissions from a diesel engine operating on FAME with fatty acid composition commensurate with that produced from several algal species currently under consideration for wide scale fuel production.