Endocrine disruptors are the substances which disrupt the normal functioning of the endocrine system by interfering with the variety of hormone-regulated physiological pathways and causing adverse health effects on the organism's physiology. They include plasticizers, pesticides, detergents and pharmaceuticals. These substances find their way into rivers and the ocean through sewage discharge and sediments at the bottom. Humans are also exposed to these toxic chemicals owing to water and fish consumption. The pelagic fish, which are bottom feeders, are at the highest risk of exposure to these harmful chemicals which settle in ocean sediments. As evidence of the threat of endocrine disrupting chemicals (EDCs) is mounting, there is a need to revise our research and improve our diagnostic efforts. With the advent of high-throughput sequencing technologies, we can now look at the complete transcriptional characterization of an organism. Sentinel fish, indicators of the environmental hazards, provide assessment for the endocrine disrupting chemicals present in the marine environment. For this thesis project, the RNA-Sequencing data of Sardine, Mackerel and Turbot were analyzed to obtain detailed snapshots of the transcriptome in both control (unpolluted) and impacted (polluted) fish. The RNA-Seq analysis of the altered expression patterns of the genes involved in important metabolic and physiological processes will provide a powerful tool for obtaining complete picture of the endocrine disruption in aquatic organisms.