Abstract: Heavy blooms frequently occurred in eutrophicated water body and Microcystis is the main algae involved in blooms.Microcystis produces a family of related cyclic hepatopeptides(microcystins, MC). These toxins are severely hepatotoxic. In this paper, a strain of Microcystis aeruginosa was isolated from a cyanobacterial bloom in the east lake and effects of ammonium and orthophosphate on its growth, chlorophyll-a(Chl. a) fluorescence and microcystins (MC) contents was investigated. Two experiment of groups were tested, with variable ammonium(0-219.6mg/L), orthophosphate concentration fixed at 4.5mg/L, or with variable orthophosphate(0-110.7mg/ L), ammonium concentration fixed at 50mg/ L. The results showed that, when orthophosphate concentration fixed, ammonium had obvious influence on the growth of M.aeruginosa. The content of Chl.a was evidently higher as ammonium concentrations ranged from 1.83 to 18.3mg/ L than those in other ammonium concentrations. The overall MC content including MC-LR and MC-RR reached the maximum at 1.83mg/ L of ammonium concentration while the content of MC-LR was much higher as ammonium concentrations ranged from 0.61 to 1.83mg/ L and the content of MC-RR was much higher as ammonium concentrations ranged from 1.83 to 18.3mg/ L. In addition, FV and MC concentration both tended to increase while the ammonium concentrations increased from 0 to 1.83mg/ L, higher ammonium concentrations restrained the growth, physiology and MC production ofMicrocystis aeruginosa. In another experiment group with fixed ammonium concentrations and increasing orthophosphate concentrations, the Chl.a content represented the decreasing tendency opposite to the increased concentrations of orthophosphate and was highly correlated with FV/ Fm(P<0.01,r= 0197). MC contents were obviously higher as the concentrations of orthophosphate were below 0.56mg/ L than those in higher concentrations. It demonstrated by the statistical analysis the MC-LR production was closely correlated to FV/ Fm(P<0.01,r= 01967).