Aquaculture has been one of the fastest growing segments of global food production sector in recent decades. With the rapid development, it also leads to many environmental problems. For example, both per unit area yield of aquatic products and their quality has declined continuously. It is important that well-balanced systems be developed that are sustainable. Constructed wetlands (CWs) are ecologically beneficial, low-cost treatment alternatives, proven capable of reducing suspended solids, 5-day biochemical oxygen demand (BOD₅), nitrogen, phosphorus and heavy metals from wastewater of many sources. In the present paper, the physicochemical and microbial characteristics of culture ponds in an Integrated Pond Recirculating Aquaculture System (IPRAS) based on constructed wetland were investigated during the period of June to October 2008. In the study, was amplified from total DNA of bacteria in water samples and followed by DGGE. Sequences of 13 dominant bands excised from DGGE gels were analyzed and the closest relatives of obtained sequences were all uncultured bacterial clone in GenBank.The results indicated that levels of dissolved oxygen (DO) and transparency (SD) showed a decreasing trend along the flow direction (P14⁺-N), total phosphorus (TP) and chemical oxygen demand (COD_Mn). The recirculating treatment increased water DO and SD, while decreased pH, COD_Mn and nutrients compared to the control. The DGGE fingerprints suggested a high species richness of microorganism and the clustering dendrogram revealed distinct differences in phylogenetic tree, the Actinobacteria, Proteobacteria, . The results of canonical correspondence analysis (CCA) also revealed that the distribution characteristics of DGGE fingerprints was strongly associated with the measured environment. Hereby, conclusions could be reached that the recirculating aquaculture system, as a new cultivation pattern, effectively improved the microbial environment of the culture ponds and benefited pond aquaculture. The results also provided basic references for analyzing the microbial community structure and their functional relationships