A 30-day experiment was conducted to investigate the effectiveness of bio-floc technology for maintaining good water quality in with average weight of ( farming ponds. The total suspended solids(TSS), total nitrogen (TN) and alkalinity (CaCO₃) were determined every 3 days and microbial communities of the bio-floc were analyzed using the PCR-DGGE (PCR-denaturing gradient gel electrophoresis) every 5 days, respectively. The results showed that water TSS concentration reached a peak value of (419.67±11.5) mg/L on the 9th day, which was significantly (<0.05) higher than that of the other time points. From the 15th day on, the TSS remained at a relatively stable level of 244.67 mg/L. The TN ranged from 6.65 to 11.15 mg/L, and it reached the peak value of (10.11±1.05) mg/L on the 9th day. There was no significant difference in TN between water after the 12th day and water at the beginning of the farming trial (>0.05). Alkalinity in the farming system ranged from 136.68 to 239.20 mg(CaCO₃)/L, which reached maximum peak value of (238.22±5.44) mg (CaCO₃)/L on the 6th day, after which it decreased gradually and then remained stable. Bio-floc had a crude protein content of 30% dry weight. The acquired sequences of 20 bands in 16S rDNA DGGE gel and six bands in 18S rDNA DGGE gel were analyzed by BLAST searches against the NCBI GenBank database. The main prokaryotic microorganisms represented by the 20 main bands in 16S rDNA DGGE gel were Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, and Bacteroidetes. throughout the process of formation of the bio-floc, and was the dominant bacteria on the 5th, 10th, and 15th days. The existence of Alcaligenaceae had some influence on the increase in water alkalinity during this period. We also found that bands 7 and12 represented C, which appeared on the 0th, 5th and 10th days; they disappeared in the late culture period, which indicated that the application of bio-floc technology can control algal growth to some extent. The main Eukaryotic microorganisms represented by the six main bands in 18S rDNA DGGE gel were sp., and belongs to the diatoms, and was present from the 1^stto 15^th days of bio-floc culture. A larger number of sp. existed at the later stage of the bio-floc culture. The results demonstrated that the bio-floc system achieved stable operation state after 15 days. Bio-floc could regulate the water quality and the distribution of bacteria and algae effectively; it could also maintain the balance and development of the whole aquaculture system.