Oxidative stress indices were measured in gills and digestive glands of Perna viridis collected from three coastal locations in Goa i.e., Bambolim, Marmugao Harbour and Malim. In addition to lipid peroxidation, the activities of antioxidant enzymes such as superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase and glutathione S-transferase and two non-enzymatic antioxidants (ascorbic acid and reduced glutathione) were investigated in order to understand their variation with respect to pollution status of the sampling locations. A significant increase in lipid peroxidation and antioxidant enzymes of both the tissues is observed at Mormugao Harbour and Malim, suggesting that the animals at these two locations are at higher level of oxidative stress as compared to those at Bambolim. Conversely, low levels of non-enzymatic antioxidants such as ascorbic acid and reduced glutathione, observed at Mormugao Harbour and Malim indicate that the animals may use these compounds to counteract stress in the tissues. This study shows that changes in lipid peroxidation, superoxide dismutase, catalase, glutathione reductase, glutathione S-transferase and reduced glutathione in tissues of P. viridis can be used as molecular biomarkers in environmental monitoring programs.