Decomposition of Microcystis is accompanied by the release of phosphorus, during which bacteria play an important role. A series of experiments were undertaken to evaluate the effect of bacteria on the decomposition of Microcystis taken from Lake Taihu, a Chinese lake that is suffering from dense Microcystis blooms. The 16 experiments involved four size fractions of colonial Microcystis from Lake Taihu, with and without the addition of lake sediment and Gram-negative bacterial inhibitor NaN3. The highest decomposition rates were recorded for the smallest size Microcystis fraction (< 25 μm) with the addition of the sediment. The lowest decomposition rates were recorded for the smallest Microcystis fraction without the sediment, but with the addition of Gram-negative bacterial inhibitor NaN3. The higher decomposition rates in the treatments with NaN3 and sediment suggest that Gram-positive bacteria in the sediment are important for the decomposition process. Additionally, higher concentrations of total dissolved phosphorus (TDP) in the treatments with NaN3 suggest that more phosphorus accumulates in the Gram-negative bacterial cells around the colony, which may be an important source of phosphorus for Microcystis cells. In the no-sediment treatments, the ratios of TDP concentration to initial TP concentration were 64%-82%. The results of this experiment suggest that both Gram-negative and Gram-positive bacteria play an important role in the decomposition of Microcystis cells and in the release of phosphorus from Microcystis colonies.