Abstract: The acute toxic effects of Cu²⁺, Cd²⁺ and Zn²⁺ on growth of the marine microalga Karenia mikimotoi and Prorocentrum minimumwere investigated. The sensitivity differences of the two alga were estimated, and the effects of different concentrations of heavy metals on growth of the bloom-forming microalga were analyzed. Moreover, a further study on toxicity of Cu²⁺ to K. mikimotoi at the sub-cellular level was conducted using the techniques of transmission electron microscope (TEM) and flow cytometry (FCM). The 48 h EC₅₀/96 h EC₅₀ of Cu²⁺, Cd²⁺ and Zn²⁺ stresses on P. minimumwere 0.514 and 0.276 mg/L, 0.835 and 1.215 mg/L, 4.376 and 7.976 mg/L, respectively. The stresses on K. mikimotoi were 1.881 and 1.881 mg/L, 5.405 and 6.268 mg/L, 13.134 and 18.732 mg/L, respectively. The results showed that:1) The relative growth rate of both populations of the two marine microalga decreased gradually with the increasing concentrations of the heavy metals, and the sensitivity was Cu²⁺ > Cd²⁺ > Zn²⁺ according to the 48 h EC₅₀ and 96 h EC₅₀. P. minimumwas more sensitive to the stress. 2) Results of FCM analysis showed that Cu²⁺ exposure significantly increased the cell volume and the complexity of the cell contents of K. mikimotoi, but it did not affect the mean fluorescence intensity (MFI) of chlorophylls a as compared to the control without Cu²⁺ stress. 3) When exposed to Cu²⁺ stress, the ultrastructure of the membrane system of K. mikimotoi was obviously damaged, while the structure of mitochondria and chloroplast showed little changes by TEM analysis.