We attempted to identify the compound responsible for the growth inhibition of Microcystis aeruginosa occurring when a culture broth of Bacillus subtilis C1 was added to the medium. The active compound was purified from B. subtilis C1 culture broth by adsorption chromatography and HPLC, and was identified as a type of glycolipid based on 1H NMR and MS analyses. The purified active compound completely inhibited the growth of M. aeruginosa at a concentration of 10 μg/ml. This is the first report of a glycolipid produced by a Bacillus strain that has potential as an agent for the selective control of bloom-forming M. aeruginosa.