The present study aimed to improve the lipid content and lipid productivity of Chlorella sp. HS2 by exposing them to ethyl methanesulfonate (EMS) to generate a mutant and followed with fluorescent assorted cell sorting (FACS) for the selection of mutant cells having desirable phenotypes. The microalgae were subjected under 100 mu mol mL(-1) concentration of EMS for 30 min, followed by intracellular lipid staining with boron-dipyrromethene (BODIPY) fluorophore for FACS based selection. The biomass growth, lipid content, lipid productivity, and fatty acid composition of the selected mutagenized strain (SMS, TE+F) of Chlorella sp. HS2 were compared against those of FACS selected strain without mutagenesis (FSS, T-F) and parent wild strain (PWS, TC), under two different carbon supplementation schemes (only CO2 supply and optimized carbon supply). The highest lipid content and productivity of 35.6% and 248.7 mg L-1 d-(1), respectively were observed in the SMS grown under optimized carbon supplementation (1% CO2 (v/v) and 0.5 g L-1 NaHCO3), which was a substantial improvement over those of FSS (26.6% and 193.4 mg L(-1 )d(-1)) and PWS (24.7% and 153.6 mg L-1 d(-1)). The fatty acid methyl ester (FAME) profile of the lipids derived from SMS showed a marked increase in the proportion of saturated fatty acids (SFA) and mono-unsaturated fatty acids (MUFA) (76.7%) over those of FSS (70.2%) and PWS (69.6%). Lastly, fuel properties were found to be appropriate for biodiesel production, as they corroborate with international fuel standards. These results indicate that directed evolution using EMS mutagenesis with FACS is a powerful tool to achieve microalgal strain improvement for biofuel production.