Concentrations of copper (Cu), iron (Fe), manganese (Mn), nickel (Ni) and zinc (Zn) in muscle and gills of four Benthic fish species (Brachirus orientalis, Argyrops spinifer, Platycephalus indicus and Sillago sihama) from Shif Island of Iran were analyzed using flame atomic absorption spectrometry. The heavy metal levels observed in tissues varied for Cu: 2.15–820.98, Fe: 24.46–533.26, Mn: 1.80–53.17, Ni: 1.86–65.54 and Zn: 28.77–375.79 mg/kg. Significant differences were found among muscle and gill of the four fish species. Heavy metals concentration were significantly (p < 0.05) higher in the gill than in the muscles of all fish species studied. The metal levels in benthic fish species should be continuously monitored in polluted areas since benthic fish indicated a tendency to bioaccumulate pollutants in their tissues from polluted water. The indices of Estimated Daily Intake, Target Hazard Quotient and Hazard Index suggests no risk while carcinogenic risk for Ni showed unacceptable carcinogenic risk.