Hypericum is a worldwide-distributed genus with almost 500 species, including the medically used, facultative apomictic species H. perforatum. It is one of the few large plant genera for which alpha taxonomy has been completed and most species have been described. To conduct a formal cladistic analysis of the genus, we coded 89 morphological characters for all described taxa and analyzed the data for the species using parsimony and Bayesian methods. The obtained trees indicate that Hypericum is monophyletic if the monotypic genus Santomasia is included, and that Lianthus is its sister. The arrangement of the remaining genera of Hypericaceae included in the analysis is in congruence with molecular phylogenies. Within Hypericum the cladistic analysis revealed a basal grade containing Mediterranean species and three big clades containing most of the diversity of the genus. In contrast to earlier assumptions, we found no indication for an African origin of Hypericum, but assume that the genus evolved in what today is the Mediterranean area. Our phylogenies indicate a shrubby habit to be the ancestral state within Hypericum from which species with tree-like and herbaceous habit evolved, and that apomixis originated at least three times independently within the genus.