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Citrus black rot is a serious disease of citrus plants caused by Alternaria citri. The current study aimed to synthesize zinc oxide nanoparticles (ZnO-NPs) by chemically or green method and investigate their antifungal activity against A. citri. The sizes of synthesized as measured by transmission electron microscope of ZnO-NPs were 88 and 65 nm for chemical and green methods, respectively. The studied prepared ZnO-NPs were applied, in vitro and in situ, at different concentrations (500, 1,000, and 2,000 μg/ml) in post-harvest treatment on navel orange fruits to verify the possible control effect against A. citri. Results of in vitro assay demonstrated that, at concentration 2,000 μg/ml, the green ZnO-NPs was able to inhibit about 61% of the fungal growth followed by 52% of chemical ZnO-NPs. In addition, scanning electron microscopy of A. citri treated in vitro with green ZnO-NPs showed swelling and deformation of conidia. Results showed also that, using a chemically and green ZnO-NPs at 2,000 μg/ml in situ in post-harvest treatment of orange, artificially-infected with A. citri, has reduced the disease severity to 6.92% and 9.23%, respectively, compared to 23.84% of positive control (non-treated fruits) after 20 days of storage. The out findings of this study may contribute to the development of a natural, effective, and eco-friendly strategy for eradicating harmful phytopathogenic fungi.