The present study was conducted to evaluate the metal induced abnormalities in the gills of Schizothorax niger (endemic fish) from Dal lake seasonally for a period of two years. The highest concentration of metals was observed in the summer seasons and the lowest concentrations in the winter seasons during the study period. Further, histochemical analysis demonstrated enormous amount of metals (Cu, Fe and Zn) in the gills of Schizothorax niger in summer seasons during the entire study period. The subsequent effects of metals, demonstrated by wet digestion-based Atomic Absorption Method and histochemcial methods showed histological changes on the gills of Schizothorax niger. The general changes in the gills of the host included oedema, congestion of the secondary lamellae with epithelial hypertrophy and hyperplasia principally at the origin of the primary lamellae or rakers with proliferation of the basal cell. Further, the apex of the secondary lamellae was often club shaped and blunt.