Abstract: A large number of microorganisms live in the phycosphere, which has an important influence on cyanobacteria proliferation. Sixty-six bacteria associated with one strain of Microcystis aeruginosa and two strains of Synechocystis spp. from Dianchi Lake were isolated by using six different mediums. Forty-six bacteria were selected for phylogenetic analysis based on 16S rRNA gene sequences. The forty-six bacteria belong to three phylums (Actinobacteria, Proteobacteria, Firmicutes), three classes, four orders, six families, seven genus, and nine species. Actinobacteria is the dominant class (73.91%), Aeromicrobium is the dominant genus (41.30%), and the dominant species is Aeromicrobium ponti (21.74%). The dominant genus of the bacteria associated with three strains of cyanobacteria were from Aeromicrobium. However, Microbacterium sp. and Sphingopyxis sp. were only isolated from the phycosphere of Microcystis aeruginosa. Nine strains affected the proliferation of Microcystis aeruginosa significantly, of which one strain showing promotion and eight strains inhibiting proliferation. L-9-3 (Sphingopyxis solisilvae) increased the number of cells of Microcystis aeruginosa by 87.62%. NIU-9-2 (Sphingopyxis solisilvae) and NIU-M-3 (Aeromicrobium halocynthiae) reduced the number of cells by 81.24%. The resource library of bacteria associated with cyanobacteria was enriched, the foundation for studying the interaction between cyanobacteria and their associated bacteria and ‘controlling cyanobacteria by bacteria’ was laid in the study.