Fenoxaprop-p-ethyl (FPE) was studied for possible ecotoxicity on two representative toxigenic cyanobacteria including Microcystis aeruginosa and Microcystis viridis. Growth curves, chlorophyll a content, protein content, microcystin levels, oxidative stress, and apoptosis rates were measured for the two cyanobacteria after exposure to different concentrations of FPE. Results showed that the changes in chlorophyll a content and protein content were consistent with cell density, and M. viridis was more sensitive than M. aeruginosa to FPE. The results of oxidative stress indicated that FPE induced the generation of malondialdehyde (MDA) and enhanced the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in these two cyanobacteria. To further explore the toxicity of FPE, apoptosis rates and toxin levels were measured for the two cyanobacteria. Different degrees of apoptosis rates were observed in the two cyanobacteria, and the apoptosis rates increased with the increase concentration of FPE. The intracellular and extracellular MC-LR were both affect by FPE. The presence of FPE in aquatic ecosystem may stimulate the synthesis and release of MC-LR, which may cause serious water pollution and pose threats to human health. These results may be useful for the ecotoxicity assessment of FPE and guiding the rational use of pesticides in agriculture.