Groupers () are part of the large fish family Serranidae and are an important marine-cultured genus. In China, groupers have been farmed for over 30 years. Innovative technologies such as recirculating aquaculture systems (RAS) have been developed to improve the efficiency and sustainability of intensive aquaculture. In RAS, bacterial communities that are critical to ecological processes are also closely correlated with diseases in aquaculture. This study aimed to clarify bacterial community characteristics in marine RAS for groupers. Water samples were collected from the following pond types:fish-production, solid-liquid separation, sedimentation, biofilter, protein-separation, ultraviolet-sterilization, and oxygen-increasing. Samples were filtered through 0.22 μm mixed cellulose ester membranes to collect microbial biomass. Bacterial community DNA was isolated from the membrane filters. High-throughput sequencing (Illumina MiSeq) of the V3-V4 hypervariable region in the 16S rRNA gene was used to investigate microbiome structural characters. The results showed that Proteobacteria was the most abundant phylum in the water supply. Other important phyla included Bacteroidetes, Cyanobacteria, Fusobacteria, Firmicutes, and Nitrospira. Principal coordinate analysis and cluster analysis indicated that bacterial composition differed significantly before and after UV irradiation. The most dominant class in the rearing, solid-liquid separation, sedimentation, and protein-separation ponds was -Proteobacteria, whereas α-Proteobacteria was the most dominant in the ultraviolet-sterilization and oxygen-increasing ponds. Both classes were dominant in the biological-filter pond. The Shannon diversity index decreased first and then increased, peaking in the biological filter pond before decreasing again to the lowest value in the ultraviolet-sterilization pond, followed by a slight increase in the oxygen-increasing pond. In addition, our analysis of the water environmental parameters showed that dissolved oxygen concentrations increased, whereas NH₃ and NO₂^- concentrations decreased, remaining low after the water was purified. This outcome suggested that the RAS system has an effective water purification process. The correlations between microbial communities and environmental parameters were also investigated with canonical correspondence analysis, which showed that phosphates, pH, dissolved oxygen, and temperature had relatively stronger effects on bacterial communities than did other measured environmental variables. Overall, however, no significant association existed between environmental factors and microbial community structure, possibly due to small sample sizes.