Effects of artemisinin (derived from Artemisia annua) on the photosynthetic activity of Microcystis aeruginosa was investigated by using chlorophyll a (Chl a) fluorescence transient O-J-I-P and JIP-test after exposure to elevated artemisinin concentration. High artemisinin concentration resulted in a significant suppression in photosynthesis and respiration. Results showed that the OJIP curves flattened and the maximal fluorescence yield reached at the J step under artemisinin stress. The decreased values of the energy needed for the RCs' closure (Sm) and the number of oxidation and reduction (N) suggested that the reduction times of primary bound plastoquinone (Q(A)) was also decreased. The absorption flux (ABS/RC) per photosystem II (PSII) reaction center and the electron transport flux (ET(0)/RC) decreased with increasing artemisinin concentration. Excess artemisinin had little effect on the trapping flux (TR(0)/RC). The results showed that the decrease of photosynthesis in exposure to excess artemisinin may be a result of the inactivation of PSII reaction centers and the inhibition of electron transport in the acceptor side.