BACKGROUND: Integration of oleaginous microalgae cultivation with wastewater treatment is considered a low-cost approach for manufacturing algae-based biodiesel. However, autotrophic microalgae cannot survive in organic wastewater where the effluent is usually turbid and sunlight cannot penetrate into the wastewater. Thus mixotrophic microalgae should be explored. The objective of this study was to investigate the potential of using mixotrophic Chlorella kessleri to produce fatty acids from organic materials. RESULTS: Results revealed that mixotrophic C. kessleri fatty acids display much greater productions (up to 54.67% of cell dry weight) and more suitable compositions for biodiesel production (moderate carbon chain length mainly with C16 and C18, down to 1.17 delta/mol of unsaturation degree) than autotrophic ones. A suitable final pH (near neutral) after nitrate-depletion and a high organic carbon consumption seemed to be the key factors manipulating fatty acids production under whichever organic substrate tested. CONCLUSION: These characteristics increase the acceptability in using mixotrophic C. kessleri as a potential easy-control candidate in biodiesel production. If fed with available organic effluent of wastewater as the nutrient supply, C. kessleri may have great potential for profitable biodiesel. (c) 2012 Society of Chemical Industry