Substrates and electron acceptors essential for microorganisms in aquaculture systems were gradually scavenged in undisturbed sediments according to the efficiency of energy metabolism along the depth, and the depth-related gradient of biogeochemical properties provided niches for metabolically diverse microorganisms. Vertical characteristics of microbial community structures may reflect the redox condition of the sediment which influences the quality of overlying water. In this study, the vertical microbial community composition of bacteria in high density culture of hybrid snakehead ponds sediment (0~50 cm) was investigated by PCR-DGGE, and the correlations between microbial communities with physicochemical characters of interstitial water were also discussed. Five phyla of bacteria including Bacteroidetes, Proteobacteria, Firmicutes, Verrucomicrobia, Planctomycetes were found. Hierarchical clustering (CLUSTER) and non-metic multidimensional scaling (MDS) analysis showed that microbial community of sediment core could be divided into three groups with significant differences, including the upper layer sediment (0~6 cm), middle layer sediment (7~38 cm) and the deep layer sediment (39~50 cm). Marglef's species richness index and Shannon-Wiener diversity index analysis of the vertical microbial communities indicated that middle layer of sediments had higher microbial diversities, which was similar to the studies of nature systems. The survey of vertical physicochemical characters of interstitial water revealed that-N concentrations ranged from 10.98 mg/L to 77.87 mg/L, increased with the sediment depth and stabilized after the depth of 15~18 cm, and PO₄^3--P concentrations ranged from 0.01 mg/L to 0.14 mg/L, declined with the sediment depth and stabilized after the depth of 9~10 cm, and the concentrations of NO₃^--N,NO₂^--N,SO₄^2--S, Fe²⁺ were relatively stable with little vertical variation. BIOENV/BEST analysis found that NH₄⁺-N was the best environment factor which had great impact on the microbial communities, then PO₄^3--P. The two factors are the main environment parameters of quality control in aquaculture water.