Sesame is an important oilseed crop. It belongs to the sesame, or pedalicum family (Pedaliaceae). The crop is known for its high oil content (up to 60% of oil), powerful antioxidants (sesamolin and sesamol) and has a wide application: pharmaceuticals, in food industry as traditional healthy food, as biofuel. Sesame oilcake (up to 10% fat and 40% protein content) is a valuable livestock feed and also can be used as fertilizer. The sesame is affected by many pathogens, most of which are seedborne and cause quantitative and qualitative changes in seed material. Plants from seeds infected with fungal pathogens can be not only affected, but also serve as foci of secondary infection. They become carriers of diseases, spreading them to new areas of growth. Identification of phytopathogens is very important for determining the mycoflora specter and seed quality. In the current work, sesame was studied by molecular methods for the presence of fungi of the genus Fusarium, A. alternata and Aspergillus flavus. To determine the infection, healthy seeds without obvious external signs of infection were selected. DNA was isolated from seeds using 2% SDS buffer (sodium dodecyl sulfate). DNA samples were tested using nested PCR (polymerase chain reaction) and genus- and species-specific primers for fungal pathogens. Seed infection of twelve sesame varieties harvested in 2021 was studied: Biolsadovski, Zaltsadovski, Leader, Manzhursky ulucsheny, Kubanets 57, Donskoy belosemyanny, Liano, Natasha, Margo, Solnechny, Gusar, Serebrysty. In all samples, pathogens A. alternata, Fusarium spp. were detected. Aspergillus flavus pathogens were detected in two sesame samples: Kubanets 57 and Natasha.