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Climatic and ecological changes, the exchange of seeds, the use of new plant protection products and plant growing technologies lead to the appearance in the regions of Russia of previously undetected species and strains of phytopathogenic microorganisms. Phytopathogens expand their ranges, adapt to the defeat of new plants, and strains that are resistant to popular pesticides appear. In our work, new types of fungi affecting potatoes (Septotinia populiperda, Ilyonectria crassa, Trichocladium sp.) And tomato (Phomopsis phaseoli, Irpex lacteus) were identified. Previously not detected in Russia strains of Rhizoctonia solani of the AG-K group, affecting potato stems in the south of European Russia, were discovered. For the first time, R. solani strains resistant to the fungicide pencycuron and capable of growing at temperatures of 35 ° C and above were discovered; the presence of thiabendazole-resistant Helminthosporium solani strains in Russia and Europe was shown. The transition from cultural and morphological criteria to molecular genetic ones in the analysis of species and intraspecific diversity made it possible to identify species and intraspecific groups of fungi of the genera Fusarium, Alternaria, Colletotrichum, confined to the defeat of potatoes, tomatoes and other plants. The differences were revealed between the strains of the section Fusarium incarnatum-equiseti, affecting tomato in Russia and Uganda. The prevalence of previously known pathogens is also changing. Thus, in the last decade in Russia and Belarus, diseases caused by the fungus Colletotrichum coccodes and the oomycete Pythium ultimum have become widespread in potatoes. Thus, a detailed analysis of phytopathogens using modern molecular methods shows constant changes in their species and intraspecific composition, which requires adjusting the plant protection schemes and predicting the development of diseases.