In-situ transesterification of microalgae lipids using microwave irradiation has potential to simplify and accelerate biodiesel production, as it minimizes production cost and reaction time by direct transesterification of microalgae into biodiesel with microwave as a heating source. This study was conducted to research the effect of microwave irradiation with in-situ transesterification of microalgae under base catalyst condition. The process variables (reaction time, solvent ratio, microwave power) were studied using 2% of catalyst concentration. The maximum yield of FAME was obtained at about 32.18% at the reaction time of 30 min with biomass-methanol ratio 1:12 (w/v) and microwave power of 450 W. The GC MS analysis obtained that the main component of FAME from microalgal oils (or lipids) was palmitic acid, stearic acid and oleic acid. The results show that microwaves can be used as a heating source to synthesize biodiesel from microalgae in terms of major components resulting.