Hydrothermal fractionation for micro-algae, Schizocytrium sp., was investigated to separate sugars, lipids, and proteins. This fractionation process produced protein-rich solid cake and liquid hydrolysates, which contained oligomeric sugars and lipids. Oligomeric sugars and lipids were easily separated by liquid-liquid separation. Sugars in the separated hydrolyzate were determined to be mainly D-glucose and L-galactose. Fractionation conditions were optimized by response surface methodology (RSM). Optimal conditions were found to be 115.5 ℃ of reaction temperature, 46.7min of reaction time, and 25% (w/w) of solid loading. The model predicted that maximum oligomeric sugar yield (based on untreated micro-algae weight), which can be recovered by hydrothermal fractionation at the optimum conditions, was 19.4 wt% (based on the total biomass weight). Experimental results were in agreement with the model prediction of 16.6 wt%. Production of bioethanol using micro-algae-induced glucan and E. coli KO11 was tested with SSF (simultaneous saccharification and fermentation), which resulted in 11.8 g-ethanol/l was produced from 25.7 g/l of glucose; i.e. the theoretical maximum ethanol yield based on glucan in hydrolyzate was 89.8%.