BACKGROUND: One of the major abiotic stressors that have a serious effect on plant growth and productivity worldwide is the salinity of soil or irrigation water. The effect of foliar application of magnetite nanoparticles (size = 22.05 nm) at different concentrations (0, 0.25, 0.5, and 1.0 ppm) was investigated to improve salinity tolerance in two wheat cultivars, namely, Misr1 (Tolerant) and Gimmeza11 (Sensitive). Moreover, toxicological investigations of magnetite oxide nanoparticle in Wistar albino rats were estimated. RESULTS: The magnetite nanoparticles positively affected growth, chlorophyll, and enzymatic antioxidants such as superoxide dismutase (SOD), stimulating reduced glutathione and improving the aggregation of several polypeptide chains that may be linked to the tolerance of saline stress. In contrast, magnetite nanoparticles reduced malondialdehyde (MDA). Inverse sequence-tagged repeat (ISTR) assay of DNA molecular marker showed the change in band numbers with the highest polymorphic bands with 90% polymorphism at primer F3, B5 and 20 positive bands in Gimmeza11 with 0.5 ppm magnetite nanoparticles. In the median lethal dose (LD50) study, no rats died after the oral administration of magnetite nanoparticle at different doses. Therefore, the iron oxide nanoparticle was nontoxic when administered orally by gavage. CONCLUSION: Magnetite nanoparticles partially helped to alleviate the effects of salt stress by activating growth, chlorophyll content, SOD, glutathione, and soluble proteins in two wheat cultivars (Misr1 and Gimmeza11) and decreasing MDA content