Effects of phosphorus limitation on the physiological and biochemical changes of the freshwater bloom alga Microcystis aeruginosa Qutz. are reported in the present study. As a result of phosphorus limitation, biomass was controlled to some extent and the protein content per cell in vivo decreased. However, the carbohydrate content per cell was higher in phosphorus limitation over the 8 d of cultivation. Soluble proteins were distinct in the media, whereas phosphorus deficiency induced the presence of a unique protein (16.2 kDa). Under conditions of phosphorus limitation, the activities of both superoxide dismutase and peroxidase per cell in vivo were lower than under normal conditions in the last cultivation. The in vivo absorption spectra of cells showed chlorophyll absorption peaks at 676 and 436 nm, over 10 nm red-shifted from the normal position; cells showed an absence of a chlorophyll c with an in vivo absorption peak at 623 nm and an extraction absorption peak at 617 nm. The chlorophyll a/carotene and chlorophyll a/xanthophylls ratios decreased under conditions of phosphorus limitation, photosynthetic efficiency (Fv/Fm) was clearly lower, and the low-temperature fluorescence emission spectra indicated a higher peak at 683 nm and a lower peak at 721 nm relatively, with the 721 nm peak drifting slightly to the red and the 683 nm peak strengthened with a weakened 692 nm shoulder peak.