Abstract: Ammonia is a naturally occurring highly toxic environmental pollutant. Lethal effects of ammonia (22 ppm) on the biochemical changes of fresh water teleost, Cyprinus carpio was studied in FT-IR spectroscopy. The fish exposed to lethal concentrations of ammonia for 96 h showed altered membrane lipids, altered protein profiles and increased glycogen were recorded. Likewise the decrease in α-helix and an increase in random coil structure were also observed when the fish was exposed to lethal concentrations of ammonia. The present study suggests that FT-IR spectroscopy on the muscle tissues on above said fish can be used as a rapid and inexpensive tool in toxicological research and are good biomarkers for field assessment in areas that are subject to a multiplicity of environmental variations.