To study the influence of microfiltration on regulating the bacterial c09ommunity structure in recirculating aquaculture systems (RAS), water samples were taken from Takifugu Rubripes farming RAS tank A-with microfiltration and tank B-without microfiltration, respectively on day 1, 30 and 60 of the experiment. The total number of Vibrio spp. and bacteria in the culture water were measured using plate counting method, then the special distribution of Vibrio and Rhodobacteraceae were detected by fluorescence in situ hybridization (FISH). Meanwhile, the bacterial community composition in the water was analyzed by 16S rDNA amplicon sequencing. The counting results showed that the total number of Vibrio in tank B was lower than that in tank A. Except for the first day of the experiment, the total number of bacteria in tank B was lower than that in tank A. The FISH detection showed that with the passage of culture time, the number of detected bacteria increased rapidly; in untreated tank A, Vibrio aggregated as dots, while Rhodobacteraceae were distributed evenly in the water, and in tank B, both Vibrio and Rhodobacteraceae  were distributed evenly in water. The 16S rDNA amplicon sequencing results indicated that there were differences in the bacterial composition and structure between untreated tank A and micro filtered tank B, with the proportion of Vibrio in tank B significantly lower than that in tank A. Except for a few fluctuation on experiment day 30, the proportion of Rhodobacteraceae in  tank B’s water was significantly higher than that in tank A’s. The alpha diversity of microflora in aquaculture water was analysed. Except for experiment on day 1, there was no significant change in bacterial abundance and diversity in the water of tank A and tank B. This paper explores the changes in bacterial populations in RAS water caused by microfiltration, and the related research results are expected to provide a theoretical reference for disease prevention and control in RAS.