Coptis chinensis contains antiseptic alkaloids and thus its rhizomes and preparations are widely used for the treatment of.fish diseases. In order to realize the risk of water ecosystems produced by this medical herb and preparations used in aquaculture, the present experiment was carried out to study the toxicity of Coptis chinensis rhizome extract (CRE) to Scenedesmus oblique and Chlorella pyrenoidosa grown in culture solution with 0.00 (CK), 0.088 (Tl), 0.44 (T2) and 1.76 mg · L(-1) (T3) of CRE, respectively. The results show that low concentration of CRE (T1) inhibited the growth rate of the alga and high CRE (T2 and T3) ceased growth and reproductions. CRE also decreased the chlorophyll and proteins in alga cells, indicating the inhibition of photosynthesis and protein biosynthesis, which could be direct reasons for the low growth rate and death of green alga. The efflux of protons and substances from alga cells led to pH reduction and conductivity increment in culture solution with CRE. Furthermore, the activity of superoxide dismutase in alga increased at the beginning of CRE in T1 and T2 treatments but decreased as time prolonged which was in contrast to high CRE treatment. And the long exposure to low CRE treatment behaved otherwise. This suggests that the low concentration of CRE could induce the resistant reactions in alga at initial time but high CRE concentration or long exposure even at low CRE concentration could inhibit the enzyme synthesis. Similarly, malondialdehyde in alga increased as CRE concentrations increased in culture solutions, implying the damage and high permeability of cell membrane. In general, Chlorella pyrenoidosa was more sensitive to CRE. The abuse of rhizomes and preparations in aquaculture and intensive cultivation of Coptis chinensis plants in a large scale might produce ecological risks to primary productivity of water ecosystems.