Superoxide dismutase (SOD) is one of the antioxidant defense enzymes in mussels and converts the superoxide anion into hydrogen peroxide and this enzyme is used as biomarkers of oxidative damage. As well as many topics in ecology, stable isotopes are also signature for organic and heavy metal pollution in aquatic ecosystems. This study aims to compare the stable carbon and nitrogen values of different mussel tissues and the changes on the SOD values of the same tissues in order to understand the relationship between two mechanisms of bioindicator processes of physiological response of mussel to pollution. The changes in SOD activity in the gill, hepatopancreas, and mantle tissues of Mytilus galloprovincialis with C-13 and N-15 isotopes were assessed in two locations (Kepez and Guzelyal) in Canakkale. The SOD values of mussel samples were found as the gill > hepatopancreas > mantle collected from Kepez and the gill > hepatopancreas collected from Guzelyal. There were no significant differences among the mean SOD values of different tissues. There was enrichment both in nitrogen and carbon isotope values of hepatopancreas tissues both in Kepez and Guzelyal samples. There was a negative correlation between both isotope values and SOD values of samples. As well as SOD values, the isotopic composition of particularly hepatopancreas tissue is a good indicator for evaluation of pollution.