Aims: Identification of bacterium HYK0203-SK02 and its lysis of Stephanodiscus hantzschii. Methods and Results: In an effort to identify a bio-agent capable of controlling S. hantzschii blooms, we used the algal lawn method to identify 76 bacteria in relevant water samples. Of these, the seven isolate showed algicidal activity against S. hantzschii; isolate HYK0203-SK02 exhibited the strongest algicidal activity, and was used for further analysis. 16S rDNA sequencing of this isolate allowed us to identify HYK0203-SK02 as a strain of Pseudomonas putida (99(.)2%). Growth of S. hantzschii was strongly suppressed by bacteria in all growth phases, with the strongest algicidal activity noted against diatoms in the exponential stage (5-18 days). Host range assays revealed that isolate HYK0203-SK02 also strongly inhibited the growth of Microcystis aeruginosa, but stimulated growth of the diatom Cyclotella sp., which has a similar structure to that of S. hantzschii. Biochemical assays revealed that the algicidal substance seemed to be localized in the cytoplasmic membrane of this newly identified algicidal bacterium. Conclusion: The algicidal bacteria P. putida HYK0203-SK02 caused cell lysis and death of not only diatom S. hantzschii but also cyanobacteria M. aeruginosa, dramatically. Algicidal substance might be located at the compartment of cytoplasmic membrane.