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Human activities generate vast amounts of wastewater, which contains various toxic metals. Microalgae are able to remove heavy metals from wastewater and accumulate lipid to produce biodiesel. In this study, the abilities to remove copper (Cu) and accumulate lipid of the green algal species Scenedesmus sp. were examined. The microalga Scenedesmus sp. was exposed to Cu concentrations of 0, 0.5, 1, 2, 5, and 10 mg/l under laboratory conditions. The results indicated that Cu inhibited the growth of Scenedesmus sp. at a 96h- EC50 of 7.54 mg/l. Furthermore, the highest removal rate was 89.5%. Lipid accumulation was increased significantly to 23.6% with the addition of Cu at 5 mg/l. The present study indicated that the green alga Scenedesmus sp. possesses the ability to remove Cu from aqueous media and accumulate lipid in its cells. Our results suggested that this species could be applied in wastewater treatment technology and biodiesel production.