The discharge of industrial effluents having heavy metals throw enormous deleterious impacts on aquatic organisms especially in fish. This potential accumulation of heavy metals in the fish tissues are subsequently transferred to human beings through the food chain. Thus, heavy metal pollution in fish has become an important worldwide concern, not only because of the threat to fish, but also due to the health risks associated with fish consumption. In this context, to investigate the extent of damage to fish tissues, FT-IR Spectroscopy can provide adequate information on the molecular composition of the fish tissues by detecting and analyzing light that is elastically scattered from the tissues following its excitation by monochromatic laser light. The present study aims to analyze the impact of industrial pollutants on the muscle tissues of Lates calcarifer inhabiting in Uppanar estuary, Cuddalore, at three different stations with respect to summer season. FT-IR spectra reveal significant differences in absorbance intensities between muscle tissues collected from three stations, reflecting the alterations in the biochemical constituents especially proteins and lipids. The spectral analysis showed variations in composition of bio molecules of the muscle tissue at a wave number region of 3423 to 701 cm-1. The results suggest that FT-IR spectroscopy could be used as a potent tool for the detection of biochemical changes that occur as a result of metal intoxication.