Aggregates are basic unit of cyanobacterial bloom, which covered by an amorphous mucilage preventing air exchange between inside and outside of aggregates, thus leading high diel variation of DO and pH. The high diel variation, abundant DOC and easy access to sunlight possibly have a selection for the bacteria inhabited within the aggregates. In this study, the composition of free-living bacterial (FLB) and attached bacterial (AB) communities in Microcystis aggregates in a eutrophic lake Taihu were compared. FLB contained significantly more Actinobacter and Pelagibacter than AB, whereas Microcystis aggregates enriched Alphaproteobacteria including Aquidulcibacter sp., Niveispirillum sp., Porphyrobacter sp., Tabrizicola sp., Rhizobium sp., Elstera sp., and Rhodoferax sp. Typical attached strains were isolated using the standard ten-fold dilution plating technique. The genomes of 10 attached bacteria and 5 free-living bacteria were sequenced and compared to reveal indications of potential typical associated bacterial properties. The genomes of assigned attached bacteria revealed distinct signaling features that differed from those detected among free-living bacteria. Genes involved in chemotaxis receptors and transport are more abundantly represented among attached bacteria than free-living bacteria. Genome analysis also revealed that 7 strains had photosynthesis gene clusters, 3 strains had denitrification gene clusters, and 1 strain had N2-fxiation clusters among the 10 attached bacteria. Physiology studies confirmed that these strains had respective abilities. Our studies suggested that strains within aggregates established beneficial (N2-fxiation and nutrient cycling), neutral (photosynthesis) or detrimental (denitrification) associations of varying intimacy with their hosts.