T iver specimens were taken from seventy fish of, Tilapia zillii9 living -■—'in three different localities in Qalyobya govemorate; unpolluted, agricultural-polluted and industrial-polluted waters of the River Nile. Water analysis was carried out to evaluate the heavy metals in these tested localities. Polymorphism of liver proteins was revealed by SDS-PAGE electrophoresis. Also, DNA damage was detected by counting the fragmentation percent. Results showed that the measured heavy metals were higher in the agricultural and industrial localities than in control; and sometimes exceeded the permissible concentrations. Fractions of liver proteins showed disappearance and polymorphism in the fish especially that was very close to the outlets of agricultural and industrial drainage water. Additionally, both agricultural and industrial pollution caused an increase in the percentage of DNA fragmentation, however the impact of industrial pollution was higher than that of agricultural pollution,The study suggested that there is clear molecular changes in T. zillii; this declares the use of these molecular parameters in diagnosing pollution.