A marine raphidophyte Heterosigma akashiwo is a causative agent of harmful microalgal blooms, which often cause the massive mortality of aquacultured finfish. In the present study, the Pacific oyster Crassostrea gigas was reared with H. akashiwo, and effect of the microalga on filter-feeding behavior and microflora of the gastrointestinal tract was investigated. The intake of the raphidophyte cells inhibited the molluscan filter-feeding activities, suggesting the negative physiological effect of the microalgal cell contents. How ever, the bivalves ingested the H. akashiwo cells to the same extent as the diatom Chaetoceros calcitrans, a non-harmful indicator to estimate the filtration rate, showing a continuation of their non-selective ingestion of the phytoplankton. Microflora of the oyster soft tissue was dominated by bacteria affiliated with the family Rhodobacteraceae, some of which are associated with microalgae. In addition, the Bacteroidetes species, in which algicidal bacteria are included, were also found in the bivalve individuals exposed to H. akashiwo. These results suggested that the ingested phytoplankton affected the microbial flora in the gastrointestinal tracts, some constituents of which helped the mollusc assimilate the ingested red tide phytoplankton. This study will provide beneficial information to clarify mechanisms by which the oyster evades the ichthyotoxicity of harmful microalgae and the participation of the intestinal microorganisms in these processes.