Abstract: Background and Objective: Dodder infestation causes a significant loss for yield and seed quality of the Egyptian clover. Therefore, the aim of this study was to measure differences between healthy Fahl plants, Fahl infested dodder and dodder at molecular level and to induce some desired mutations of Fahl ecotype for more tolerance/resistance to dodder infestation using gamma irradiation. Material and Methods: In the first experiment, 100 seeds of Fahl ecotype were planted with different dodder rates. The growth parameters were recorded at the harvest time. The random amplified polymorphic DNA (RAPD) analysis using ten primers was performed to investigate the relationship between Fahl healthy plants (control), infested Fahl with dodder and dodder at the molecular level. In the second experiment, series of Fahl ecotype (100 seeds each) were irradiated with gamma-ray doses of radioactive cobalt 60 (60Co) and infested with different levels of dodder DSPP. The isozymes analysis was used to measure variation in Fahl treated with gamma-ray. Results: There were a negative correlation between level of dodder infestation and the growth parameters. The RAPD analysis showed unique markers in Fahl infested by dodder with primer OP-R03, OP-Z10, OP-B20, OP-B06, OP-A08 and OP-A012. The isozymes fractionation showed variation among irradiation doses especially for glutamic oxidase transferase, peroxidase and malate dehydrogenase. Conclusion: These results showed that growth parameters of Fahl ecotype has been decreased with increasing the level of dodder infestation. RAPD analysis showed some interaction between Fahl and dodder infestation. There were no significant differences among gamma ray doses used in this study. Therefore, Further investigation is needed, including different doses of gamma radiation to induce mutation in the Egyptian clover Fahl ecotype that provides more tolerance/resistance to the dodder infestation.