In this study the thermo-resistant green alga Micractinium sp. ME05 was cultivated in media containing molasses as a carbon source. Shake flask experiments and 2-L bioreactor experiments were conducted at different inoculum ratios, aeration rates, and agitation speeds. The experimental condition which resulted in the highest biomass concentration (3.73 +/- 0.45 g L-1) with 10% inoculum in 500-mL flasks was scaled up to 2-L flasks at two aeration rates (0.25 and 0.5 L min(-1)). An increase in biomass concentration from 2.35 +/- 0.53 to 3.06 +/- 0.21 g L-1 was observed with an increase of aeration rate from 0.25 to 0.50 L min(-1), which demonstrated significant effect of aeration rate on biomass concentration (p = 0.000 < 0.05). In 2-L bioreactor experiments, highest biomass productivity (0.53 +/- 0.076 g L-1 day(-1)) and lipid productivity (7.7 +/- 1.6 g L-1 day(-1)) were obtained with 5% (v/v) inoculum and 50 rpm agitation speed. The principal fatty acids were palmitic acid (C16:0) and linoleic acid (C18:2) comprising 30.2 +/- 1.01 and 45.2 +/- 1.32% of the total fatty acid content, respectively. Thus, the present study highlights the possibility of using molasses for biomass and lipid production with Micractinium sp. ME05 under different cultivation conditions. Using low cost feedstock such as molasses would be valuable in terms of evaluating waste materials for further biodiesel production.