In this study is shown the usefulness of molecular diagnostics (PCR) of fungal pathogens in selected varieties of cultivated plants. This study indicates of using SCAR-PCR assay as a rapid, reliable method of identification of fungal pathogens: Oculimacula acuformis, O. yallundae, Septoria tritici, fungi of genus Microdochium and Fusarium, in plant cultivation, taking as an example cereals and rape.