Present investigation aimed to assess the alterations in branchial architecture of Ctenopharyngodon idellus exposed to chlorpyrifos. 96 h LC50 of chlorpyrifos to C. idellus was found to be 7.24 µg/L. Fish were exposed chronically to 2.41 and 1.44 µg/L sublethal concentrations (ecologically relevant concentrations) of chlorpyrifos for 15, 30 and 60 days. The gills of the CPF exposed fish showed partially affected secondary lamellae with shortening and curling, increased inter-lamellar space, sloughed off epithelium, hyperplasia and necrosis of pavement cells. On 60 days exposure, more pronounced degenerative changes, including severe necrosis, hyperplasia and hypertrophy of pavement cells, eroded and uplifted lamellar epithelium were noticed. Ultrastructural alterations include distorted nucleus and mitochondria in pavement cells, marked contraction in cisternae of golgi complex. Particularly in chloride cells, abundant mitochondria with distorted shape and size, dilation in between their cristae and tubular network were observed. The severity of damage was more profound at 60 days exposure. Thus, the observed cytopathological lesions of fish gills can be used as sensitive biomarkers for pesticide contamination.