A procedure for compositional characterization of a microalgae oil is presented and applied to investigate a microalgae based biodiesel production process through process simulation. The methodology consists of: proposing a set of triacylglycerides (TAG) present in the oil; assuming an initial TAG composition and simulating the transesterification reaction (UNISIM Design, Honeywell) to obtain FAME characterization values (methyl ester composition); evaluating deviations of experimental from calculated values; minimizing the sum of squared deviations by a non-linear optimization algorithm, with TAG molar fractions as decision variables. Biodiesel from the characterized oil is compared to a rapeseed based biodiesel.