Florfenicol (FF) and thiamphenicol (TAP) are two typical pharmaceuticals used widely as therapeutica antibiotic agents in aquaculture. However, little is known about the potential adverse effects of these two antibiotics on non-target organisms in the aquatic ecosystem. In this study we investigated the effects of FF and TAP on photosynthesis and the antioxidant system of the cyanobacteria Microcystis flos-aquae. Over a concentration range of 0.001-1μg/L, the results showed that both FF and TAP significantly increased the chlorophyll a content of M. flos-aquae, while the superoxide dismutase (SOD) activity, catalase (CAT) activity and the levels of malondialdehyde (MDA) changed slightly. In contrast, the chlorophyll a content of M. flos-aqua was significantly inhibited (p<0.01) at high concentrations (>1μg/L) of FF and TAP, reaching a 46% inhibition level at 50μg/L FF and 56% inhibition at 100μg/L TAP. At the same time, the activities of SOD and CAT along with MDA content also increased significantly (p<0.01), indicating that the high concentrations of both FF and TAP led to oxidative stress in the algae. In addition, the M. flos-aquae fluorescence parameters (Fv/Fm, Fv/Fo, alpha, ETRmax and Ik) increased with increasing concentration of both FF and TAP, which may be the result of the increasing photoprotection capacity.