Phenetic and phylogenetic relationships in genus Helianthus were assessed by molecular markers. Forty taxa belonging to 36 species and 4 unclassified accessions of Helianthus were studied using the RAPD technology. Single ten mer primers were screened for those amplifying fragments common to species belonging to one section or common to all species of the genus. Sequence homology between RAPD fragments of the same size was confirmed by molecular hybridization. Most of the fragments were found to be of the same size in other species and to share the homology indicated by molecular hybridization. Out of 118 retained fragments, 33 were common to all Helianthus species, 56 were unique to perennial species of which 24 were unique to sect. Atrorubentes, 29 were unique to sect. Helianthus, whereas 0 were unique to sect. Ciliares. The presence/absence of RAPD (fragments or signal hybridizations) were used to determine all structures using correspondence analysis and to compute genetic distances. Correspondence analysis clearly separated the 3 sections and recognized some series. The Jaccard distance and the Sokal and Michener similarity were chosen with UPGMA and Neighbor Joining Method to construct phenetic trees which were very similar to those of the current taxonomy. The simple method used to characterize these fragments led to powerful tools to use RAPD for help in taxonomy.