In this study, the concentrations of mercury in the oyster Crassostrea madrasensis (Preston) and sediment collected from Cochin Backwater were monitored from eight different stations. Mercury was analysed by cold vapour absorption in a mercury analyser. The levels of mercury in the oyster samples ranged from 15 to 48 ppb for smaller size and 7.0 to 37.0 ppb for larger size group, whereas the concentrations of mercury in the sediment samples were higher than in the oyster. The concentrations of mercury in sediment samples ranged from 31 to 144 ppb. However, the concentration of mercury in smaller size oyster was higher than that in the larger size oyster. The concentrations of mercury in the oyster and sediment samples were higher in summer than in monsoon. Generally, higher concentrations were observed in sediment followed by the smaller and larger size oysters during the study period.