The present study was carried out to determine the effect of Malathion (an organophosphate) on electrophoretic patterns of proteins in the gill and liver tissues of freshwater fish Channa punctatus (Bloch). The fish were exposed to 2% sub lethal concentration of pesticide Malathion at different time intervals i.e. 24 h; 48 h; 72 h and 96 h for a period of 10 days. The changes in the tissue proteins of vital organs such as gill and liver were examined on 7.5% of SDS –PAGE. The protein patterns indicated that the gill tissue has higher number of Electrophoretic protein bands compared to liver tissue and control. Gill tissue shown 9 protein bands in control. After exposed to Malathion (Organophosphate) gill tissue exhibited 8 bands at 24h, 6 bands at 48h, 4 bands at 72h and 2 bands at 96h. And the liver tissue showed 8 protein bands, after exposed to Malathion (OP) 8 protein bands at 24h, 5 bands at 48h, 4 bands at 72h and 2 bands at 96h. The results shown that the number of protein bands and their intensity were decreased in gill and liver of test fishes than in control the protein banding patterns were identified by standard marker protein and Rm values were calculated.