The present study was focused on the impact of chlorpyrifos(CPF) on the expression of electrophoretic protein patterns and metabolism of protein in the tissues of Cyprinus carpio, Fingerlings of C. carpio were subjected to various chlorpyrifos concentrations ranging from 0.1mg/L to 0.7 mg/L for 96 hr, and acute toxicity was 0.32 mg/L. Based on the LC50 value, the Cyprinus carpio were exposed to two sub-lethal concentrations viz., sub-lethal 1 (1/5th of LC50, 0.0636mg/l) and sub-lethal 2 (1/10th of LC50,0.0318 mg/l) in a semi-static system for 21 days. SDS-PAGE and estimation of protein metabolic rate were performed at the end of the exposure period to assess the changes within tissues of the liver, muscle, and gill, brain, the study has suggested that the degradation of protein caused due to proteolytic activity and oxidative stress of CPF would alter the set of genes resulting in impaired protein synthesis. The intensity of protein subunits in chlorpyrifos-exposed tissues decreased, and some protein subunits disappeared. Thus the variations in protein banding patterns and reduction in the metabolic rate are due to improper amino acid incorporation into the polypeptide chain or proteolysis which is attributed to functional and physiological alterations in cellular proteins. CPF can attack single domain proteins as well as multiple domains proteins at both concentrations thus it is categorized as a hazardous pesticide in the world.