The present study was conducted to measure and compare the concentration of mercury in Mudskipper (Periophthalmus waltoni) and Flat fish (Cynoglossus arel), which had been caught from the Bandar-e-Emam and Bandar Abbas (Summer, 2008). These fish were used as a Bioindicator to examine and compare the effect of mercury of the Bandar-e-Emam Petrochemical plant on the species of Bandar Abbas. The study used Mercury analyzer A400 for mercury measurement. The average of the mercury concentration in flat fish from Bandar-e- Emam was 0.68 mg/Kg and for the Bandar Abbas it was 0.14 mg/Kg. This showed a meaningful difference between them. The average of the mercury concentration in Mudskipper from Bandar-e-Emam was 0.81 mg/Kg and for the Bandar Abbas it was 0.07 mg/Kg which, in turn, showed a meaningful difference between them. The concentration of the Bandar-e-Emam and Bandar Abbas had a meaningful difference.