Effects of electrolysis by low-amperage electric current on the chlorophyll fluorescence of Microcystis aeruginosa were investigated in order to reveal the mechanisms of electrolytic inhibition of M. aeruginosa. Thresholds of electric current density were found under a certain initial algae cell density. When the current density was higher than the threshold density, the growth of algae was inhibited completely by electrolytic treatment, and the algae lose its ability to survive and to grow. The changes of chlorophyll fluorescence parameters demonstrated that when the algal solution was treated by current densities lower than the threshold density, PS Ⅱ of algae was damaged by electrolysis, but it still maintained relatively high activity. The activity of algae recovered completely after 6 days' cultivation. Moreover, when algal solution was treated by current densities higher than the threshold density, the connection of phycobilisome and PS Ⅱ core complexes were destroyed. PS Ⅱ system of algae was damaged irreversibly, and algae could not survive thoroughly. The inactivation of M. aeruginosa by electrolysis can be attributed to irreversible separation of phycobilisome from PS Ⅱ core complexes and the damage of PS Ⅱ of M. aeruginosa.