Potato virus Y Potyviridae (PVY) is one of the most destructive viruses of the potato crop in Egypt and the world. Ribosome inactivating proteins (RIPs) isolated from Mirabilis jalapa and Phytolacca sp plants, which inhibit the infection with necrotic tuber necrosis strain of potato virus Y (PVY^NTN) by depurinating from the 28S RNA. The primary objective of this work, was the development of an easy and simple strategy for controlling PVY^NTN by applying of aqueous extract from M. jalapa and Phytolacca sp plants. In addition, assessment of genetic diversity among PVY^NTN resistance, susceptible and the control potato plants was performed by Random amplified polymorphic DNA (RAPD). Five potato cultivars (‘Cara’, ‘Diamond’, ‘Nicola’, ‘Selan’ and ‘Spunta’)  sprayed with aqueous extracts before virus inoculation led to inhibition of PVY^NTN infection with 100%; these results were confirmed by Double antibody sandwich enzyme linked immuno-sorbent assay technique (DAS-ELISA). Analysis of variance displayed there were no significant differences in the number, weight and volume of tubers between extract-pretreated potato plants and the healthy control in all five potato cultivars. RAPD analysis using five arbitrary decamer primers was applied to determine DNA polymorphism among the PVY^NTN resistance, diseased and the control potato plants.  A total of 65 reproducible fragments ranged from 100-1200 bp were recorded using five primers. Thirty-three out of 65 (50.77%) loci were polymorphic and other 32 (49.23%) were monomorphic. The number of amplicons for each primer varied from 5 to 22 bands. Among the 65 bands, 18 (27.69%) were reproducible and considered as reliable RAPD markers for further analyses. Aqueous extract treated potato cultivars which gave resistance against the PVY^NTN strain diversified considerably using the five primers of RAPD-PCR, whereas the ‘Selan’ cultivar showed to have the highest number of specific bands (seven), followed by ‘Spunta’(six), ‘Nicola’ (five) and ‘Diamond’ (four), while ‘Cara’ scored the lowest number of unique bands (one). This information should be taken into consideration in future breeding programs. Spraying of aqueous extract from P. americana, P. acinosa and M. jalapa plants in different crops led to prevent or control viral infection.