At present, the energy consumption of Korea is increasing due to the increase of population density. Such an increase in energy consumption leads to a rise in oil prices and depletion of fossil fuels, and increases the concentration of carbon dioxide in the atmosphere, thereby causing serious environmental pollution. It is necessary to develop new and renewable energy to overcome this. The purpose of this study is to establish the optimum conditions of lipid-extraction using harmful green algae in the four rivers to substitute a petroleum and fossil fuels, and to investigate the possibility of using them as biodiesel. The antigreen-tide substances developed in the previously reported research papers were treated on the harmful green algae, and the flocculated and floating harmful green algae were collected. After drying, the optimal extraction conditions were confirmed according to the presence of various solvents and the ultrasonic treatment. As a result, in the chloroform/methanol/water mixed solvent, the most lipid was extracted and it was confirmed that it was most suitable for utilization as biodiesel when converted to fatty acid methyl ester (FAME) using extracted lipid under this condition. These results suggest that if the harmful green algae of the four major rivers are recycled, they can be utilized as next generation energy.