Nowadays, microalgae are widely discussed as a promising feedstock for biodiesel production due to the legitimate concerns about the consequences of using edible oils. Selection of the most suitable microalgal species relies on several key parameters such as growth rate, lipid productivity and fatty acid profile. In the present study, different species of Scenedesmus were isolated and compared for their efficiency as biodiesel feedstocks. S. obliquus showed the highest biomass productivity of 0.102 g CDW L−1 d−1 at stationary phase. However, S. intermedius showed the highest significant lipid content of 400.9 mg g−1 CDW. Regarding lipid productivity, S. obliquus was the most lipid productive strain at stationary phase with up to 24.94 mg L−1 d−1, representing 23.9% significant increase over that of S. intermedius. In addition, cetane number and iodine value of S. obliquus FAMEs were 54.12 and 110.3