BACKGROUND: The novelty of this work is the estimation of the fuel properties of biodiesel, a comparison study with conventional sources of biodiesel commonly used as feedstock, and an investigation for meeting the requirements of the standard specifications for this fuel produced by six strains of microalgae (three cyanobacteria, two green algae and one diatom), cultivated photosynthetically in a bubble column photobioreactor. Lipid productivity and biofuel quality were the criteria for species selection. RESULTS: Chlorella vulgaris was found to be the best strain for use as a feedstock for biodiesel production and for this specie, a carbon dioxide sequestration rate of 17.8 mg L-1 min(-1), a biomass productivity of 20.1 mg L-1 h(-1), a lipid content of 27.0% and a lipid productivity of 5.3 mg L-1 h(-1) were obtained. Qualitative analysis of the fatty acid methyl esters demonstrates the predominance of saturated (43.5%) and monounsaturated (41.9%) fatty acids. The quality properties of the biodiesel were an ester content of 99.8%, a cetane number of 56.7; an iodine value of 65.0 g l(2) 100 g(-1); a degree of unsaturation of 74.1% and a cold filter plugging point of 4.5 degrees C. CONCLUSION: The results indicate that among the fuel properties tested, the microalgal biodiesel complies with the US Standard (ASTM 6751), European Standard (EN 14214), Brazilian National Petroleum Agency (ANP 255) and Australian Standard for biodiesel. (C) 2010 Society of Chemical Industry