The freshwater cyanobacteria, Microcystis sp., commonly form large colonies with bacteria embedded in their mucilage. Positive and negative interactions between Microcystis species and their associated bacteria have been reported. However, the potential role of bacteria in the production and degradation of cyanobacterial secondary metabolites has not been investigated. In this study, a Microcystis-associated bacterial community was isolated and added to the axenic M. aeruginosaPCC7806 liquid culture. After 3years of cocultivation, we studied the bacterial genetic diversity adapted to the PCC7806 strain and compared the intra- and extracellular concentration of major cyanopeptides produced by the cyanobacterial strain under xenic and axenic conditions. Mass spectrometric analyses showed that the intracellular concentration of peptides was not affected by the presence of bacteria. Interestingly, the produced peptides were detected in the axenic media but could not be found in the xenic media. This investigation revealed that a natural bacterial community, dominated by Alpha-proteobacteria, was able to degrade a wide panel of structurally varying cyclic cyanopeptides.