Pollution with antibiotics poses a great risk to aquatic ecosystems. Although some toxic effects of antibiotics on photosystem II (PSII) have been documented, their toxicity to photosystem I (PSI) is still unclear. In this study, effects of ofloxacin on activities of both PSI and PSII of Microcystis aeruginosa (Kützing) Kützing were investigated. Exposure to 0.1 mg L⁻¹ ofloxacin led to increases in contents of chlorophyll a and carotenoids and photosynthetic activity of M. aeruginosa. PSI activity and its electron transport were not affected by 0.1 mg L⁻¹ ofloxacin. When M. aeruginosa was exposed to ≥10 mg L⁻¹ ofloxacin, the electron transport rates of PSI and PSII, the yield of cyclic electron flow (CEF) and the contribution of linear electron flow (LEF) to PSI decreased whereas Y(NA) (limitation of donor side of PSI) and Y(NO) (the quantum yield of non-regulated energy dissipation in PSII) significantly increased. CEF had a significant contribution to alleviating the inhibitory effect of ofloxacin on PSI of M. aeruginosa treated with low concentrations of ofloxacin. The protective role CEF for tolerance of PSI to the toxicity of ofloxacin decreased with increasing ofloxacin concentration.