There is a growing interest in biodiesel as an alternative fuel for diesel engines because of the high oil prices and environmental issues related to massive greenhouse gas emissions. Nowadays, microalgal biomass has become a promising biodiesel feedstock. However, traditional biodiesel production from microalgae consumes a lot of energy and solvents. It is necessary to use an alternative method that can reduce the energy and alcohol consumption and save time. In this study, biodiesel production from Chlorella protothecoides oil by ultrasound assisted transesterification was conducted and effects of reaction parameters such as methanol: oil ratio, catalyst/oil ratio and reaction time on fatty acid methyl ester yields were investigated. The transesterification reactions were carried out by using methanol as alcohol and potassium hydroxide as the catalyst. The highest methyl ester production was obtained under the conditions of 9:1 methanol/oil mole ratio, 1.5% potassium hydroxide catalyst in oil, and for reaction time of 40 min. It was also found that catalyst/oil molar ratio was the most effective parameter on methyl ester yield according to statistical data. The results showed that ultrasound-assisted transesterification may be an alternative and cost effective way to produce biodiesel efficiently.