Microorganisms play important roles in biogeochemical cycling such as organic matter decomposition and energy transformation. Recently, rapid development of aquaculture has caused a large influx of introduced organic matter into Xiangshan Bay, Zhejiang Province, China. At the same time, many ecological problems have developed in this coastal site. Study of the influence of aquaculture on microbial diversity in sediments is important for the structural and functional assessment of coastal ecosystems. In this paper, sediments in three sites were investigated in July 2011: a control or check site (CK), an intersection site 6-8 km from the aquaculture site (IS), and a cage culture site (AC). As the physicochemical background showed, total organic carbon in those three sites was different. Several physiochemical factors (T, pH, Eh and SO₄^2-) were analyzed. The temperatures of sediments in Xiangshan Bay decreased with depth, but remained between 23.0-26.5 ℃ in the upper 55 cm layer. The pH of sediments was slightly alkaline, but was elevated slightly in the AC site, although all of the sediments had pH values of 7.6-7.9. The effect of aquaculture on SO₄^2- was not significant. However, as expected, the measurement of Eh showed sediment in the CK site had the highest oxidation-reduction potential. Following with physiochemical analysis, the structure and diversity of bacterial communities in sediments from Xiangshan Bay were analyzed by Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis and cloning/sequencing. Total nucleic acids was extracted from the sediment core. T-RFLP analysis was conducted after amplification of the bacterial 16S rRNA partial gene using a fluorescent primer pair 27-FAM/907R and digestion by Msp I (C^CGG). A bacterial 16S rRNA partial gene clone library was constructed using DNA extracted from the upper 5 cm sediment layer of the CK region, and the phylogenic relationships were analyzed using the neighbor-joining method in ARB software. Our results revealed sediments from Xiangshan Bay had a highly diverse bacterial community, mainly including Proteobacteria, Firmicutes, Gemmatimonadetes, Actinobacteria, Thermomicrobia, Nitrospirae, Acidobacteria, Fusobacteria, Bacteroidetes, Planctomycetes and OP11. Thermomicrobia was the most abundant group in all sediments and layers, while the abundance of Proteobacteria was elevated in the surface layer of the CK site, making up as much as 23.7% of the clone library. The diversity index H' is an effective method of assessing microbial diversity. In this study, the diversity index H' was calculated based on T-RFLP relative abundance results. Generally, the bacterial diversity indices were CK > IS > AC. Surface layer sediments in the CK site showed the highest bacterial diversity (H'=3.83±0.01). The lowest diversity (H'=3.01±0.27) was in the 50-55 cm deep sediment in the AC site. The evenness indices were stable in the CK site (around 0.93), but also decreased in the AC site, especially in deeper layers. In the IS site, both diversity indices and evenness indices were intermediate between the CK and AC sites indicating the cage culture not only changed Eh and pH in sediments in Xiangshan Bay, but also decreased their bacterial diversity and changed the structure of the bacterial community. The bacterial community of coastal sediments was changing from a stable, highly diverse structure to an unstable structure with low diversity. Human activity such as aquaculture imports large amounts of organic matter, which not only modifies natural conditions but also leads to systemic simplification of the bacterial ecosystem. Sustainable and environmental friendly aquaculture methods should be searched for and found.