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. Tests were performed on a 2.4 L, 56 HP John Deere 4024T, non-road diesel engine meeting USEPA Tier 2 emissions regulations. The engine was fitted with a unique, low-volume fuel injection system that enabled emissions tests to be conducted with very low volumes of specialty fuel sample. Tests were performed on 9 different fuel blends at 2 different engine loading conditions. Exhaust gas measurements were made using a 5-gas emissions analysis system that includes chemiluminescence measurement of NO, NO₂ and total NO\x, flame ionization detection of total hydrocarbons and non-dispersive infrared detection of CO and CO₂. An FTIR was used to measure additional hazardous air pollutants such as formaldehyde. Particulate matter was characterized on-line, using an Aerodyne Aerosol Mass Spectrometer (AMS), which is capable of direct measurement of both particle size (50 and 1000 nm) and chemical composition. Smaller PM size distributions (10 to 100 nm) were measured using a Scanning Mobility Particle Sizer. Total PM mass emissions and the ratio of elemental carbon to organic were measured using gravimetric sampling. Results showed that the emissions from the two simulated algal methyl ester formulations were similar to those measured from soy and canola methyl esters with the exception of NO emissions which were shown to decrease for the simulated algal methyl esters. The decreased NO emissions from the simulated algal methyl esters were accompanied by a decrease in premixed burn fraction.