Vibrio alginolyticus is a globally distributed opportunistic pathogen that causes different degrees of disease in various marine organisms. According to previous studies, modified clay (MC) could effectively flocculate and reduce the density of Vibrio in water, but it is still unknown whether MC inhibits growth and how it affects virulence in bottom flocs. Here, we studied the response mechanism of V. alginolyticus in flocs treated with MC at the transcriptome level.