• Background and Aims The genus Centaurea has traditionally been considered to be a complicated taxon. No attempt at phylogenetic reconstruction has been made since recent revisions in circumscription, and previous reconstructions did not include a good representation of species. A new molecular survey is thus needed. • Methods Phylogenetic analyses were conducted using sequences of the internal transcribed spacers (ITS) 1 and 2 and the 5·8S gene. Parsimony and Bayesian approaches were used. • Key Results A close correlation between geography and the phylogenetic tree based on ITS sequences was found in all the analyses, with three main groups being resolved: (1) comprising the most widely distributed circum-Mediterranean/Eurosiberian sections; (2) the western Mediterranean sections; and (3) the eastern Mediterranean and Irano-Turanian sections. The results show that the sectional classification in current use needs major revision, with many old sections being merged into larger ones. A large polytomy in the eastern Mediterranean clade suggests a rapid and recent speciation in this group. Some inconsistencies between morphology and molecular phylogeny may indicate that hybridization has played a major role in the evolution of the genus. • Conclusions Phylogenetic analysis of ITS has been useful in identifying the major lineages in the group, and unraveling many inconsistencies in the sectional classification. However, most recent groups in the eastern Mediterranean clade are not resolved and reticulation in the western Mediterranean group of sections makes phylogenetic relationships within these two groups somewhat obscure.