Indian coastal waters are subjected to considerable pressure from sewage and industrial wastes, which are responsible for the contamination of the waters with consequent loss in biodiversity. Monitoring methods adopted so far have helped in documenting the level of contaminants in water, sediments and biota, but not the interaction of these pollutants with living organisms. Exposure of animals to xenobiotics brings disturbances in metabolic function, activating detoxifying enzymes and the antioxidant system, as also damage to genetic material. This could be used as potential biomarker to measure pollution stress in animals. While extensive work on biomarker research is being undertaken in several parts of the world, such studies are yet to receive sufficient attention in India. Marine bivalves such as clams, Mytelid mussel and oysters, which represent the entire Indian coast and are sentinel species, are considered to be the best organisms for such studies. This article stresses the importance of biomarker research and recommends incorporating the same in Indian coastal monitoring programmes.