Pyraclostrobin (PYR) is widely used in agriculture to control fungal infestations. However, the toxic effects of PYR on aquatic organisms remain poorly understood. In this study, common carp were exposed to 0.5, and 5.0 μg/L PYR for 30 days to evaluate the chronic effects on gill health via histopathological, biochemical, molecular, and metabolomic analyses. The findings revealed that exposure to PYR resulted in significant histopathological alterations, suppression of mitochondrial complex III activity, and excessive production of reactive oxygen species (ROS), including O