Recent environmental changes through oligotrophication have promoted the recovery of seagrass beds, and its ecosystem functions can contribute not only to climate change mitigation but also to climate change adaptation for oyster farming. To test the hypothesis that seagrass beds could improve the safety and environmental sanitary conditions in oyster farming areas, we conducted DNA analyses of seawater from inside the shells of cultivated Pacific oyster spat and ambient seawater from areas with and without seagrass beds. The analyses revealed that the amount of total bacteria and Vibrio spp. in both inner shell seawater and the ambient seawater were substantially lower at the sites with seagrass than at the sites without seagrass. The apparent reduction in the amount of Vibrio spp. would be an important mitigation effect of seagrass against the reduced growth and high mortality of oyster spat caused by climate change.