ABSTRACT A large number of studies have explored the effects of various nanoparticles (NPs) on different economically important plant species. In this study, yellow medick plants were grown for five weeks using hydroponics with the addition of Fe3O4 NPs at 1, 2 and 4 mg/L. Plant morphology, chlorophyll a, genotoxicity and expression of miR159c, one of the most important plant miRNA that is involved in plant response to fungal infections, were investigated. The results indicated that Fe3O4 NPs significantly increased plant root length (9%–32%), chlorophyll a fluorescence (1.94–2.8-fold), miRNA expression (0.31–0.42-fold), induced genotoxicity and reduced genome stability (12.5%–13.3%), compared to those of the control. The study demonstrated that Fe3O4 NPs simultaneously induce genome instability in yellow medick and increase expression of miR159c. Therefore, Fe3O4 NPs can be used to increase plant resistance to fungal diseases, such as powdery mildew.