The aim of the present study was to obtain a marine bacterium active against Karenia mikimotoi from the East China Sea and to characterize its extracellular algicidal substances. Using preparative high-performance liquid chromatography (prep-HPLC) and electrospray ionization/quadrupole-time of flight mass spectrometer coupled with a high-performance liquid chromatography (LC/MS-Q-TOF) system, we purified the alga-lysing substance produced by strain ZR-2 and determined its molecular structure. Based on morphology and l6S ribosomal DNA (rDNA) sequence analysis, the ZR-2 strain was highly homologous to Thalassospira species. Algicidal activity against K. mikimotoi was detected in the cell-free filtrate but not in bacterial cells. The alga-lysing substance produced by ZR-2 was ethanol-soluble and thermostable, with a retention time of 6.3 min and a measured elemental composition of C7H5O2 ([M-H](-) ion at m/z 121.0295). The alga-lysing substance produced by ZR-2 was determined to be benzoic acid. Compared with the negative control, both purified ZR-2 bacteria-free filtrate and standard benzoic acid promoted K. mikimotoi cell disruption and induced K. mikimotoi cell content leakage. Our study is the first to report benzoic acid activity against K. mikimotoi as well as production of benzoic acid by a Thalassospira species.