Mercury, a global pollutant, has become a real threat to the developing countries like India and China, where high usage of mercury is reported. Mercury and other heavy metals deposited in to the aquatic system can cause health risk to the biota. The common edible fishes such as Mugil cephalus, Arius arius, Lutjanus ehrenbergii, Etroplus suratensis were collected from Cochin backwaters, Southwest India and analysed for mercury and other heavy metals (zinc, cadmium, lead and copper) in various body parts. Kidney and liver showed highest concentration of metals in most fishes. The omnivore and bottom feeder (E. suratensis) showed high concentration of mercury (14.71 mg/kg dry weight) and other metals (1.74 mg/g-total metal concentration). The average mercury concentration obtained in muscle was 1.6 mg/kg dry weight (0.352 mg/kg wet weight), which is higher than the prescribed limits (0.3 mg/kg wet weight). The concentration of other heavy metals in the muscles of fishes were found in a decreasing order Zn>Cu>Cd>Pb and are well below WHO permissible limits that were safe for human consumption. Metal selectivity index (MSI) obtained for all the metals except mercury showed that both carnivores and omnivores have almost same kind of affinity towards the metals especially Zn and Cd, irrespective of their feeding habit. The MSI values also indicate that the fishes have the potential to accumulate metals. High tissue selectivity index (TSI) values were reported for kidney, muscle and brain for all metals suggests that the metal concentration in these tissues can serve as an indication of metal polluted environment. Even if the daily intakes of Zn, Cd, Pb and Cu from these fishes are within the provisional maximum daily intake recommended by WHO/FAO, the quality is questionable due to the high hazard index obtained for mercury (>1). Fishes like E. suratensis being a favourite food of people in this region, the high consumption of it can lead to chronic disorders as this fish has high concentration of metals.