Effects of potassium permanganate (KMnO4) on PSII of Mycrocystis aeruginosa were investigated by measuring the chlorophyll fluorescence in vivo. KMnO4 exposure reduced the rate of oxygen evolution and cell growth. High concentration of KMnO4 (10 mg L −1 ) decreased the fast phase and increased the slow phase of QA − reoxidation kinetics. Electron transport after QA was blocked, resulting in a considerable amount of QA − reoxidation being performed via S2(QAQB) − charge recombination. KMnO4 decreased the density of the active photosynthetic reaction centers and the maximum quantum yield for primary photochemistry and inhibited electron transport, which resulted in a decline of the performance of PSII activity and caused an increase in dissipated energy flux per reaction center and antenna size. Our results suggest that both the donor side and the acceptor on the phase of QA − to QB to PQ of PSII in M. aeruginosa were targets of KMnO4 toxicity.Additional key words: fluorescence relaxation kinetics; inactive reaction center; S-state test. Abbreviations: ABS/RC, TR0/RC, ET0/RC, DI0/RC -absorption, trapped, electron transport and dissipated energy flux from the antenna per reaction center, respectively; Fv -the maximal variable fluorescence; OEC -oxygen-evolving complex; P680 -primary electron donor of PSII; PIabs -performance index; PQ -plastoquinone; RC -reaction center; RC/CS0 -amount of active PSII reaction centers per cross section; S2(QAQB) -QAQB − state with the S2 state of the water-oxidizing complex; φP0, φE0, φD0 -quantum yields of electron transport in PSII reaction center to QA, from QA − to plastoquinone and in energy dissipation, respectively; ψ0 -probability that the electron reaches electron carriers after QA − .