We evaluated the bacterial community structure in water collected from several mariculture zones in Sanggou Bay in summer 2007 using PCR-DGGE. Some of the bands were shared by two or more stations, while others were unique to a particular location. Based on the DGGE profiles, we distinguished four areas, including a no-culture area (outer bay), kelp farming area (bay-mouth), integrated mariculture area (majority of the area in the middle of the bay), and a mollusk monoculture or fish farming area (bottom of the bay). The highest similarity in the bacterial community structure was between the scallop and oyster culture areas (94%), while the lowest was between the no-culture and mollusk monoculture or fish farming area (41%). Sequence analysis of twelve major bands from the DGGE profiles revealed that these sequences were highly similar to those of Proteobacteria, including class Alpha and Gamma proteobacteria. The similarity of the nucleotide sequences ranged from 92% to 98%. Roseobacter, which can remove nitrogen-containing pollutants, was only present in the fish farming area. Our results suggest that seaweed culture had a lower impact on the environment then shellfish monoculture and fish culture. Thus practicing IMTA can reduce the degree of pollution from shellfish and fish monoculture.