The method of direct organogenesis has been successfully used for overcoming the inability for crossing between Helianthus annuus (cv. Albena) and Verbesina helianthoides (genus Verbesina). As a result of long-term individual selection in the hybrid materials, fertility restorer lines were produced in the R 10 generation. The applied molecular method (RAPD) confirmed the hybrid nature of the obtained breeding material and indicated an introgression of Verbesina helianthoides DNA into some of the hybrid progenies produced. Using the similarity coefficient of Nei and Li (1979), a dendrogram was generated through UPGMA analysis with the aim to determine the genetic distance of the studied genotypes. We were able to demonstrate that RAPD could be used for characterization of intergeneric hybrid progenies in sunflower at a late stage of selection (F9) in which an increased genetic variation was discovered.