Epiphytic bacteria associated with colonial Microcystis may play an important role in the development of cyanobacterial bloom. However, information on characterization of Microcystis-associated bacteria is limited. In this study, eighteen Microcystis-associated bacteria which belonged to six bacterial groups: Alpha proteobacterium, Beta proteobacterium, Gamma proteobacterium, Actinobacteria, Cytophagia and Flavobacteriia, were isolated from four Microcystis species (M. wesenbergii, M. flos-aquae, M. firma and M. aeruginosa). Analysis by BIOLOG plate indicated that except for two isolates of Alpha proteobacterium and one isolate of Actinobacteria, the other isolates were capable of utilizing more than 10 carbon sources. Among 18 bacterial isolates, 12 isolates showed chemotaxis, 12 isolates displayed hydrophobicity, and 14 isolates exhibited autoaggregation ability. Except for Flavobacteriia, other five groups contained hydrophobic bacterial isolates. All six groups contained bacterial isolates with chemotaxis and autoaggregation ability. Most of bacterial isolates associated with each Microcystis species were capable of utilizing more than 10 carbon sources, and exhibited hydrophobicity. For each Microcystis species, there was at least one group of bacterial isolates exhibiting coaggregation ability. Except for M. flos-aquae, most of bacterial isolates associated with each of other three Microcystis species showed chemotaxis. The results indicated that active metabolic potential, chemotaxis, hydrophobicity, and the abilities of autoaggregation and coaggregation might help the bacteria colonize the Microcystis colonies.