Abstract Fungal pathogens can significantly reduce the potential yield of agricultural crops, especially cereals. One of the most dangerous are pathogens of the Fusarium genus. They contribute to the infestation of plants, reduction of yields, and contamination of agricultural crops with mycotoxins, which are harmful to human beings and animal health. The absence of active substances, the problem of pathogen resistance to fungicides, and the pressure of society to limit the use of chemical plant protection products are the most important issues in agriculture. This has resulted in research aimed at finding natural methods to control plant pathogens gaining importance. One of them is the use of essential oils. In laboratory experiments, clove essential oil and pine essential oil were used. The influence of different concentrations of the above-mentioned substances on the development of the mycelium of Fusarium species (F. equiseti, F. poae, F. culmorum, and F. avenaceum) was analyzed and the germination of wheat and maize seeds infected with the pathogens of the genus Fusarium was assessed. Clove oil significantly inhibited the growth of mycelium of the Fusarium species and reduced germination parameters than pine oil.