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The quantification of fangchinoline and tetrandrine in water extract of Stephania tetrandra and their effects on Chlorella pyrenoidosa were performed. The result showed that the fangchinoline content varied from 59.2-71.6 g kg-1 dry weight in water-extracted solution of Stephania tetrandra. The content of tetrandrine were between 40.7and 46.3 g kg-1 dry weight. Exogenously added fangchinoline and tetrandrine inhibited the growth of Chlorella pyrenoidosa respectively, with EC50,6d of 12.44 mg L-1 and 9.90 mg L-1 (6 days). The EC50,7d of Stephania tetrandra extract on Chlorella pyrenoidosa was 10.02 mg L-1 (7 days). Furthermore, the extract of Stephania tetrandra did not change pH, turbidity, electrical conductivity and chlorophyll a obviously, indicating that Stephania tetrandra, as a kind of algicides, did not remarkably impact the safety of aquatic ecosystem. Therefore, we concluded that Stephania tetrandra might be a potential effective method in control and mitigation of harmful algal bloom.