Recently many species of algicidal microorganisms including viruses, bacteria, amoeba etc. have been detected in and after the peak of the harmful algal blooms such as dinoflagellates, raphidophytes and diatoms. These microorganisms are divided into two major types: gliding bacteria and amoeba which directly attack host algal cells after cell-to-cell attachment, and eubacteria which kill or lyse these algae through toxic substances excreted by these bacteria. The former are Cytophaga, Saprospira as gliding bacteria and Labyrinthula, while the latter are Flavobacterium, Alteromonas, Vibrio and others. Some algicidal substances have been isolated and purified, but are not yet identified. To investigate the behavior of algicidal bacteria during algal bloom, the RFLP analysis of 16S rDNA was conducted, and 4 of 17 RFLP types usually comprised the major flora in the disintegration of Heterosigma akashiwo red tide. Use of RFLP patterns and DNA probes of 16S rDNA and monoclonal antibodies as an ecological tool for ecological research and prevention of harmful algal blooms is being studied.