In order to reveal the characteristics of bacterial community in the cyanobacterial blooming pond, the water samples in the cyanobacterial blooming ponds and the control ponds were collected from four aquaculture farms located in Guangdong, Yunnan and Guizhou Provinces, respectively. Both the physicochemical factors and biological indicators were analyzed. By applying polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique,the differences in bacterial community structure in these water bodies were found. The bacterial community diversity in aquaculture water were analyzed according to the abundance of PCR-DGGE fingerprint bands, and conducted an unweighted pair group method with arithmetic mean (UPGMA) cluster analysis on the bacterial community structure in the water body. The results indicated that the PO₄-P content was significantly higher in cyanobacterial blooming pond than that in the control pond (P<0.01).Linear regression analysis revealed a positive correlation between PO₄-P and the content of chlorophyll a (Chl.a), which represents the degree of cyanobacterial blooming (R²=0.869, P<0.01).The analysis of physicochemical factors in combination with the redundancy analysis (RDA) in bacterial community indicated a close relationship between PO₄-P and bacterial community in aquaculture water. While no significant difference in bacterial community diversity was seen between cyanobacterial blooming pond and control pond (P>0.05), significant differences in bacterial community structure between the two ponds existed. Further sequencing analysis revealed that the characteristic bacteria in the cyanobacterial blooming pond was Flexibacter, which might play a role in algal pyrolysis. The Synechococcsus content was significantly lower in the cyanobacterial blooming pond than that in the control pond. This reduced Synechococcsus content might be related to the inhibition of Synechococcsus growth by the substantial blooming of Microcystis.