Using allelochemicals produced by macrophytes to control harmful algae is a novel antialgal method. The present research investigated effects of the species-specific antialgal allelochemical EMA on activities of antioxidant enzymes of Chlorella pyrenoidosa and Chlorella vulagaris. The results showed that 0.25 mg/L of EMA increased activities of superoxide dismutase (SOD), peroxidase (POD)and catalase (CAT) of C. pyrenoidosa and C. vulagaris. With the increase of EMA concentrations, activities of the 3 enzymes of C. pyrenoidosa decreased sharply. The activity of SOD of C. pyrenoidosa decreased to 0 when the EMA were 4 mg/L. With the increase of EMA concentrations, activities of the 3 enzymes of C. vulagaris increased to as higher as 3-4 folders of that of the control set. The results gave hints to elucidate the species-specific antialgal mechanisms of EMA.