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The non-judicious use of pesticides sprayed in the agricultural lands ultimately finds their way to aquatic ecosystems. The Aquatic ecosystems face the threat of biodiversity loss due to toxicity induced by these agro-chemicals. Other than targeted pests, pesticides affect a wide range of non-target organisms, such as invertebrates and fish inhabiting aquatic environments. Among various physiological changes, histopathological alterations in fish intestines due to organophosphate toxicity is the basic tool for finding the potency of these chemicals in mitigating fish health. Therefore the present study deals with the impact of Chlorpyrifos on histopathology of the stomach of C. punctatus in which set of twelve fish were exposed to 0, 5, 2.5, 3.5, 4.5, 5.5 and 6.5 µl/L concentration of Chlorpyrifos. The lethal concentration (LC50) value of Chlorpyrifos was calculated as 4.5 µl /L for 96 hours of exposure. The fish were exposed to three sublethal concentrations (0.15, 0.25 and 0.35 µl/L) of Chlorpyrifos for 15 and 30 days respectively. Fishes showed severe histological changes in stomach. The degenerative changes included degeneration of serosa layer, columnar epithelium and goblet cells were analysed and a section of stomach also showed loosely arranged of muscle layers, large vacuolation in the mucosa as well as in the sub mucosa region. Presence of scattered blood cells in the submucosa and muscularis layer of the stomach tissue was also observed. This clearly demonstrates that the sublethal concentrations of Chlorpyrifos have a deleterious effect on the stomach of C. punctatus. Therefore the pesticide can be considered as a potent toxic pollutant to fishes whose entry to natural waterbodies should be checked from all point and non-point sources.