Microcystis bloom is the most common harmful bloom. Microcystis cells in bloom aggregate into colonies, which is crucial for maintaining their ecological advantage. Dispersing Microcystis into the unicellular form can decrease their competitive advantage, and has been used as a strategy to control Microcystis bloom. In this study, five polysaccharide-degrading bacteria (PDB) with the ability to decompose the extracellular polysaccharides of Microcystis were screened by using bacterial polysacchrides xanthan gum and the extracellular polysaccharides of Microcystis flos-aquae as the carbon sources. The effects of the bacteria on the extracellular polysaccharides of unicellular strain M. flos-aquae, and on the colony size of colonial strain M. wesenbergii were observed by co-culture. The results showed that four strains of bacteria were able to significantly reduce the viscosity of the extracellular polysaccharides of M. flos-aquae. All five strains were able to reduce the colonial size and to inhibit the growth of M. wesenbergii. The PDB were identified to the genus Pseudomonas by 16S rDNA. This study showed that the PDB have the potential to control Microcystis bloom.