Responses of photosystem I and II activities of Microcystis aeruginosa to various concentrations of Cu2+ were simultaneously examined using a Dual-PAM-100 fluorometer. Cell growth and contents of chlorophyll a were significantly inhibited by Cu2+. Photosystem II activity [Y(II)] and electron transport [rETRmax(II)] were significantly altered by Cu2+. The quantum yield of photosystem II [Y(II)] decreased by 29 % at 100 μg L−1 Cu2+ compared to control. On the contrary, photosystem I was stable under Cu2+ stress and showed an obvious increase of quantum yield [Y(I)] and electron transport [rETRmax(I)] due to activation of cyclic electron flow (CEF). Yield of cyclic electron flow [Y(CEF)] was enhanced by 17 % at 100 μg L−1 Cu2+ compared to control. The contribution of linear electron flow to photosystem I [Y(II)/Y(I)] decreased with increasing Cu2+ concentration. Yield of cyclic electron flow [Y(CEF)] was negatively correlated with the maximal photosystem II photochemical efficiency (Fv/Fm). In summary, photosystem II was the major target sites of toxicity of Cu2+, while photosystem I activity was enhanced under Cu2+ stress.