The diversity of bacterium in the spotted scat(Scatophagus argus) rearing water by recirculating aquaculture system was investigated. Two groups of water samples, A and B, were taken from one week and one month rearing water. Bacterium in the water samples were enriched by membrane filtration, their bacterial 16S rDNA was extracted, were sequenced by MiSeq high throughput sequencing. The resultant 16S rDNA were subject to Clustering analysis, which generated 15 259 valid tags for the two smaples. With 9 092 for A sample and with 6 167 for B sample. These sequences were clustered to 90 OTUs (operational taxonomic units) with 97% similarity. The analysis of diversity indices indicated that the diversity of A sample were significantly greater than that of B sample. The species composition analysis showed that the species of bacterium in the samples covered 8 Phylums, 16 Classes, 28 Orders, 38 Families and 48 Genera. Among them, Thalassospira and Vibrio in Proteobacteria were dominating in sample A, with relative abundance of 14.51% and 13.29%, respectively; Aureispira and Dyadobacter in Bacteroidetes were dominating in sample B, with relative abundance of 44.67% and 13.29%, respectively. This study may indicate that the growth of fish, the accumulation of soluble metabolites and dissolved organic matters, changed the environment of growth of bacterium and caused population succession and adaptation.