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The present study was aimed to report the toxicity of the chlorpyrifos, an organophosphorus insecticide, with regard to histological and cytological effects through light and transmission electron microscopes in the gills of freshwater fish, Anabas testudineus. The fish were exposed to 0.125 (5% of 96 h LC), 0.250 (10% of 96 h LC), and 0.375 mgL (15% of 96 h LC) of chlorpyrifos for 7, 14, and 21 days for light microscopy and 21 days for transmission electron microscopy. The histological effects were seen in all exposed concentrations of 0.125, 0.250, and 0.375 mgL. These effects increased with the increase in chlorpyrifos concentrations and duration of exposure. The main histological effects visible in the gill tissue were fusion of secondary lamellae and epithelial hyperplasia. Other effects included the epithelial hypertrophy, lifting of lamellar epithelium, aneurysm, necrosis, and desquamation of epithelial cells were also reported. Cytological effects included epithelial detachment, large subepithelial space, necrotic cells, apoptotic remnant of cells, the presence of macrophages, swelling of mitochondria in the chloride cells, distension of the tubular system, the presence of some large vacuoles, deposition of excessive mucous, and nucleus abnormalities. This study confirms that varying doses of chlorpyrifos have adverse histological and cytological effects in the gills of A. testudineus.