Riceblast caused by Magnaporthe oryzae is the major biotic stress influences rice yield. The current investigation aimed to estimate the antifungal activity and phytotoxicity effect of different concentrations of ZnO nanoparticles (0.0, 10, 25, 50, 100 and 200 mg/L) on M. oryzae and rice cultivar Sakha101 using morphological, biochemical and molecular markers. Five ISSR markers and seven RAPD primers were utilized to estimate the potentiality effects of ZnO nanoparticles (NPs). The effect of different rates and applications of ZnO NPs used to control rice blast disease and improve grain yield were estimated in the field during 2017 and 2018 growing seasons. The results showed that, in vitro antifungal assay of ZnO NPs showed a significant decrease in colony formation in comparison to control. Foliar application of ZnO NPs at 25 mg/L was the most effective treatments for mitigation rice blast at five days before inoculation. While under field conditions, foliar spray with 25 mg/L at nursery increased the grain yield to 4.366 ton/fed in season 2017 and to 4.625 ton/fed in 2018. Foliar spray with ZnO NPs of rice offer a practical and useful approach to improve rice grain yield and reduce leaf blast disease when applied at optimal concentrations. ZnO NPs at lower concentrations (10 and 25 mg/L) enhanced seed germination and improved seedling growth, while the higher concentrations (100 and 200 mg/L) resulted in phytotoxicity. ZnO NPs treatments altered the expression patterns of seeds storage protein; induced newly synthesized isoforms and disappearance of existing ones. The obtained results using molecular markers confirmed that the lower concentrations of ZnO-NPs (10 and 25 mg/L) are considered as a good enhancement agent, as in case of rice cultivar Sakha101, using UBC 825 primer with 306 bp at concentration of 25 mg/L and OPA-9 primer with 948 bp at concentration of 10 mg/L. For M. oryzae the same trend of effects was appeared in case of UBC 880 primer with 994 bp at concentration of 25 mg/L and OPO-10 primer with 268 bp at concentration of 10 mg/L. In general, these results suggested that lower concentrations of ZnO NPs could be applied as an effective nano fertilizer for sustainable agriculture and food safety, and moreover, utilized as antifungal agent for rice blast disease.