AbstractBackgroundSensitivity differences to chemical pollutants in different phytoplankton species may potentially shape the community structure of phytoplankton. However, detailed information supporting the understanding of sensitivity variations between phytoplankton species is still limited.ResultsTo investigate sensitivity differences between the cyanobacterium Microcystis aeruginosa, and the green alga Chlorella sp. to paraquat, multiple physiological parameters were measured and compared through acute and chronic toxicity assays. Early photosynthetic responses during acute toxicity assays showed that paraquat affects Photosynthesis System II energy fluxes in M. aeruginosa within 3?h of exposure, but not in Chlorella sp. After 5?h of cumulative exposure, an EC50 based on the maximum quantum yield for primary photochemistry of 0.54?mg L?1 was achieved and remained more or less constant, while the EC50 values for Chlorella fluctuated around 44.76?±?3.13?mg L?1 after 24?h of exposure. During chronic 96?h exposure to paraquat, differences in antioxidant enzyme activities, reactive oxygen species (ROS) levels, and ultrastructure were observed in both M. aeruginosa and Chlorella sp. An increase in the intracellular levels of ROS and the number of plasma membrane damaged cells was observed in M. aeruginosa in the 0.2, 0.5, and 1.0?mg L?1 treatments (p?