In order to investigate the potential effect of algicidal (algae-killing) bacteria on zooxanthellae, some bacterial strains having algicidal properties were isolated from a coral community in the south of Kochi Prefecture (Japan) and their effect on freshly isolated zooxanthellae from Acropora formosa and zooxanthellae in culture (CCMP 2466-Symbiodinium goreaui (Trench et Blank)) was observed. Out of twenty bacterial strains isolated, three strains (strain 4-2DW-1, strain 4-1SW-1 and strain 1B) were found to have strong algicidal activity towards zooxanthellae with considerable cell degradation in up to five different grades (transparent/bleached cells, shrunken cells, swollen cells, necrosis and degradation). In case of freshly isolated zooxanthellae, the algicidal activity of strains 1B, 4-2DW-1 and 4-1SW1 affected 64-86%, 48-67% and 56-75.4% of cells respectively. However, in case of cultured zooxanthellae CCMP 2466-Symbiodinium goreaui (Trench et Blank), only 8-11% of zooxanthellae cells were affected. The results of this study indicate the presence of algicidal bacteria in coral communities, which can influence the health condition of zooxanthellae and suggests that algicidal bacteria might be playing a role in bleaching of corals susceptible to bacterial attack.