Abstract:An enrichment culture showing specific algae-lysing activity was isolated from the mixtures of different samples and Microcystis aeruginosa. The process of algal lysis was monitored by chlorophyll measurement, PCR, and denaturing gradient gel electrophoresis (DGGE). The result showed that the enrichment culture had still high algicidal activity against M. aeruginosa after 1/100000 dilution. Rubritepida sp. C1, Pseudomonas sp. C2 and Sphingomonas sp. C3, as accompanying bacteria, existed in M.aeruginosa. The bacterial community in M. aeruginosa showed significant change after adding the enrichment culture, where uncultured Flavorbacterium sp. A2, Sphingomonas sp. C3 and Hydrogenophaga sp. A3 were observed, and A2 became a dominant species. The obvious correlation can be seen between change of bacterial population and extinction of M. aeruginosa. Compared identification of pure bacterium with sequencing of DGGE band, it was inferred that uncultured bacteria were probably play an important role in controlling the growth and abundance of M. aeruginosa.