The Study on Hemibagrus nemurus (Valenciennes, 1840) gills was designed to investigate the influence of monogenean irritation coupled with water quality condition of the pond (earthen pond) in Perlok, Pahang. Three hundred and eighty fish host were examined, their gills were excised and fixed in 3% glutaraldehyde for scanning electron microscopy and in bouin’s solution for histology. In the infected fish gills, the pathological alterations observed such as proliferative, degenerative and necrotic changes in the epithelium of gill filaments. In the secondary lamellae, telangiectasia, fusion of secondary lamellae and excessive mucous cells proliferation were observed. Correlation was made between water quality parameters and intensity of monogenean infestation in the ponds. It can be concluded that gill alterations as a result of monogeneans irritation and poor water quality in fish ponds may serve as a sensitive biomarker for pollutants.