The inactivation behavior of two Bacillus thuringiensis bacteriophages (A8 and R3) was studied to evaluate their potential as viral indicators for disinfection by heat, UV-C, gamma rays, chlorine, isopropanol and ethanol. The heat effect was highly efficient, PFU/ ml was decreased from 12 log (non- treated) to 1 log at 55 ˚C for 90 min, while 60˚C was completely inactivated at 20 min. It was suggested that this killing effect may due to nucleic acid denatured. UV-C and Gamma irradiation were also dramatically decreased of PFU/ml. The lowest effect of tested biocides was for chlorine which supplied as sodium hypochlorite, isopropanol come in the second order. The ethanol at 80% concentration was inactivated all phage A8 population in 90 min and phage R3 in 15 min. In general, phage R3 was sensitive to tested agents than phage A8. The ability of two inactivated phages to transfer ampicillin resistance gene was studied, this ability was decreased with temperature increased. It was totally inactivated with 60 ˚C. Two phages were able to transfer the marker gene at all UV-C, Gamma and chlorine treatments. Isopropanol and ethanol were completely inactivated the process, it was suggested that this effect due to alteration of nucleic acid and structure of phages. The effects of some physical agents (UV-C and gamma rays) only were studied to identify DNA polymorphism through RAPD-PCR analysis in comparison to the control of the two selected bacteriophages. The result of RAPD analysis indicated the appearance of DNA polymorphic bands in response to treatments with doses of all gamma irradiation. Some bands present in the control disappeared in treated bacteriophages or vice versa.