Channa punctatus is commonly known as snake head fish of carnivore feeding habit. The cypermethrin pesticide is widely used in agricultural field for the control of insect pests and is coming under synthetic pyrethroids which have shown strong pesticidal activity in freshwater teleost fish, Channa punctatus. The fishes were exposed to sub lethal concentration, 0.04 mg/L (1/10th of LC50=0.4 mg/L) of cypermethrin for a period of 15, 30 and 45 days. Changes on the protein and nucleic acid levels of gill, liver and kidney tissues of Channa punctatus were observed. The results showed that, the protein content in all the tissues (gill, liver and kidney) have decreased significantly (p<0.05) when compared to control with the increase in the period of exposure to the toxicant. In the case of nucleic acids, the DNA content was found to increase significantly (p<0.05) in gill and liver tissues, but in the kidney, it was found to be in a decreased trend. Whereas, the RNA content of all the tissues (gill, liver and kidney) have decreased significantly (p<0.05) when compared to control with the increase in the period of exposure to the toxicant. Biochemical changes induced by pesticidal stress lead to metabolic disturbances, retardation of growth and reduction in the fecundity and longevity of the organism.