Glyphosate may have dual effect on bloom algae as a phosphorus source or pesticide. The physiological and biochemical responses of Microcystis aeruginosa (M. aeruginosa) to glyphosate and its formulation in the common herbicide, Roundup ® , were compared. The result suggested that both the cell numbers and Chl-a content of M. aeruginosa increased when the glyphosate concentration increased from 0.01 to 5mg P L −1 . However, Roundup ® showed low-dose (below 1mg P L −1 ) stimulation and high-dose (above 1mg P L −1 ) inhibition on M. aeruginosa cell density and Chl-a content (hormesis effect). Phosphate was more available than glyphosate or Roundup ® , and Roundup ® was more toxic than glyphosate itself at 3mg P L −1 . Analysis of the maximum yield of PSII indicated that glyphosate stimulated the photosynthesis process while Roundup ® inhibited the photosynthesis of M. aeruginosa. The photosynthesis process was enhanced on the 21st day compared with that on the 14th day in all P mediums. The extracellular alkaline phosphatase activity (APA) decreased with the increasing glyphosate or Roundup ® concentration. The change pattern of APA was similar in both the glyphosate and Roundup ® mediums.