The abundance and diversity of species within the genus Helianthus offer numerous and rewarding possibilities to sunflower breeders. All annual species and a large number of perennial species may be crossed to the cultivated sunflower by the conventional hybridization method. On the other side, the divergence and heterogeneity of the genus cause considerable difficulties, such as cross-incompatibility, embryo abortiveness, sterility and reduced fertility in interspecific hybrids. Because of that, methods of somatic hybridization, “in vitro” embryo culture, chromosome doubling, etc. are frequently used for interspecific crossing. Cytogenetic studies are used for determinations of chromosome number and structure and analyses of meiosis (microsporogenesis) and pollen viability, making it possible to establish phylogenetic relations between wild sunflower species and the cultivated sunflower and enabling the use of the former in sunflower breeding. Cytogenetic studies of the sunflower have evolved from cytology, through cytotaxonomy and classic cytogenetic to cytogenetic-molecular studies. Most intensive progress of cytogenetic studies has been associated with the use of interspecific hybridization in sunflower breeding.