【Aims】: The application of selenium nanoparticles (SeNPs), including mitigating biotic stress factors in plants, was discussed, but the influence of SeNPs on yellow lupine growth and the concentration of defence-related phytohormones such as jasmonic acid (JA) and salicylic acid (SA), during the seed germination stage and development of the seedlings of Lupinus luteus L. cv. Diament and Lupinus luteus L. cv. Mister, and during the cross-talk of SeNPs and pathogenic fungus Fusarium oxysporum f.sp. lupini, has not been studied. Additionally, the aim of this study was also to investigate the changes in concentrations of phytohormones such as giberelic acid (GA3 and GA4) and indole 3-acetic acid (IAA), playing important roles in the seed germination stage. Moreover, it was important to check whether the application of SeNPs had an impact on limiting the development of infection and Fusarium wilt.【Methods】: The experimental protocol used in this study was based on a model system: germinating seeds pretreated with SeNPs, or not pretreated, were inoculated with an F. oxysporum f. sp. lupini spore suspension or non-inoculated, and were transferred to hydroponic grow boxes containing Hoagland medium.【Results】: The analytical results of the QuEChERS method showed significant changes in concentration of defence-related phytohormones and GA3, GA4 and IAA concentrations, in SeNPs, Fusarium and SeNPs+Fusarium variants, in both Diament as well as Mister varieties. Moreover, the results of our research demonstrated that SeNPs induced better turgor of the embryo axes and the roots and limited the development of infections and fusariosis in comparison to the control. 【Conclusions】: The results provide a basis for further understanding the mechanisms of interaction of SeNP itself as well as SeNPs and F. oxysporum in the host plant.