Physicochemical and benthos data were collected from 12 marine monitoring stations in Daya Bay, during 2001-2004. 12 stations in Daya Bay could be grouped into three clusters: cluster I consisted of stations in the southern part of Daya Bay (stations S1, S2 and S6); cluster II consisted of stations in the cage culture areas (stations S3, S4, S5 and S8); cluster III consisted of stations in the southwest, the middle and the northeast of the Bay (stations S7, S9, S10, S11 and S12). Calculation with bivariate correlations between benthos and major physicochemical factors showed that the density of benthos in all stations correlated positively with temperature, DO, pH, NH4-N, SiO3-Si, SiO3-Si /PO4-P and chlorophyll a and was negatively correlated with salinity, Secchi, COD, NO3-N, NO2-N, TIN, PO4-P, TIN/PO4-P and BOD5. Factor analysis showed that there were high positive loading salinity, Secchi and NH4-N of three clusters. Results revealed that temperature, DO, pH, SiO3-Si and SiO3-Si/PO4-P and chlorophyll a could also play an important role in determining the biomass of benthos in Daya Bay, especially near the Nuclear Power Plants, in the southern part and in the cage culture areas.