A comparative study was conducted on concentration of heavy metals including: Hg, Cd and Pb in the muscle of Otolithes ruber in Abadan and Bandar Abbas Ports in the Persian Gulf. In this study, a total of 42 specimens of Otolithes ruber were collected from coastal waters of Abadan and Bandar Abbas Ports in 2010. Heavy metals were extracted from the muscle tissues using wet digestion method and concentration of metals were measured by Atomic Absorption Spectrophotometer. The results showed that mean (±SD) accumulation of Hg, Cd and Pb in the muscles of Otolithes ruber in Bandar Abbas were 0.058±0.001, 0.279±0.056 and 0.668±0.077mgKg-1 wet weight, and in Abadan were 0.056±0.007, 0.25±0.038 and 0.638±0.087mgKg-1 wet weight respectively. No significant differences were found in concentrations of Hg, Cd and Pb in the muscle of Otolithes ruber between Abadan and Bandar Abbas ports. Accumulation of these metals were higher in the muscle of Otolithes ruber than that Bandar Abbas Port. Concentration of Hg in the muscle of Otolithes ruber was lower than acceptable limit suggested by WHO, MAFF, NHMRC. However concentrations of Pb and Cd were higher