Increasing industrial development in the Masan Bay area of Korea over the past decades increased the risk for the survival of marine organisms in the bay area by the deterioration of the water quality. Since living organisms have the ability to adapt contamination-associated stimuli by the alteration of gene expression, changes in proteins can be used as an important criterion for assessing the levels of environmental conditions. In this study, therefore, alterations of the expression of proteins in the muscle of Limanda yokohamae from Dukdong and Dotsum in the bay area were surveyed and characterized as compared with Haegumgang, which served as a control site. The results demonstrated that the twenty spots detected from Dukdong and Dotsum were similar to each other. Fifteen proteins were found to be predicted or undefined proteins, while five proteins were identified as heavy polypeptide 11 of myosin, apolipoprotein A-I, fibroblast growth factor 17b precursor, G protein-coupled receptor kinase 1 b and bonnie and clyde. These data suggest that local fish in the bay area have dysfunction in muscle physiology including contraction, lipid metabolism, proliferation and differentiation and nervous system.