Microalgae are potential candidates for the production of valuable products, such as renewable biodiesel, health products and pigments. However, low biomass productivity has restricted their large-scale applications. In this study, the effects of two auxins (one natural type of indole-3-acetic acid (IAA) and the other synthetic type of 2,4-dichlorophenoxyacetic acid (2,4-D)) on the growth and fatty acid methyl esters (FAMEs) production of a freshwater microalgae Scenedesmus sp. LX1 were investigated. Both auxins showed a "low dosage-promotion and high dosage-inhibition" effect on the growth and FAMEs accumulation. The optimum dosage of IAA and 2,4-D were 1 mg L-1 and 0.1 mg L-1, respectively. Moreover, the IAA could increase the monounsaturated fatty acid content. The auxins may promote the growth by enhancing the photosynthetic activity through increasing chlorophyll contents. Therefore, auxin significantly enhanced microalgal growth and FAMEs accumulation, and has a potential for application in developing efficient microalgal cultivation.