The structure and composition of the bacterial community associated with buoyant Microcystis colonies were monitored during the decline of a cyanobacterial bloom (from October 13, 2009 to January 27, 2010). When temperature decreased, the ratio between the colony-associated bacteria and the Microcystis gradually decreased as estimated by a quantitative real-time polymerase chain reaction (qRT-PCR)-based approach. Diversity of bacterial communities was determined through denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Cluster analysis of the DGGE profiles showed that most of the bacterial communities associated with Microcystis colonies collected on the nearby dates were clustered together. The bacterial clones from four clone libraries in different months were classified into 5, 12, 6 and 12 operational taxonomic units, most of which were affiliated with Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes. Shift in dominance from pathogenic Aeromonas sp. to Shewanella sp. capable of remineralization of many organic materials was observed, and both species seemed to be associated with Microcystis colonies along with the bloom decline. These results indicated that the potential harmful effects of the Microcystis bloom on the safety of lake water during the decline period should be taken into account.