Gills are the important and sensitive organs of fish which are exposed to many environmental factors. This study was conducted to investigate the histopathological alterations of the gills of the rainbow trout cultured in one the farms of Chaharmahal and Bakhtiary in Iran. In summer of 2011, massive mortality (over 70 percent) was occurred in these fishes. With the primary examination of affected fishes, the gill samples were collected and placed in formalin 10% then sent for histopathological tests. It was distinguished that the impact of influent water polluted by rural waste water having high pH and ammonia led to gill alterations. Several histological changes were observed in the gills that included proliferative of mucosal cells, degenerative and necrotic changes in the epithelium of gill filaments and secondary lamellae, detachment of epithelium layer in primary lamella, lamellar fusion, edema in secondary lamellae, dilation and congestion in blood vessels of gill filaments. These histopathological findings suggest that influent water in considered farm with high ammonia and pH causes severe damage to the respiratory organs and consequently impact on the physiological status and incidence of mortality in fishes.