The bulk of genera within the Cardueae is placed in the subtribes Carduinae and Centaureinae, which together probably form a monophyletic group. Especially within the Carduinae, the phylogenetic relationships are unclear. The elucidation of generic affinities within the group is of both evolutionary and systematic interest: understanding the basal relationships could give insight in the diversification processes, the place of origin and the relative age of individual subgroups. It would further contribute to clarify subtribal classification, since it is not clear whether the Carduinae are monophyletic or paraphyletic with the segregation of the Centaureinae. Eventually, genus delimitation could be tested in the case of larger complexes of closely related genera. In order to reconstruct phylogenetic relationships, DNA sequence data of the Internal Transcribed Spacer (ITS) regions of the nuclear ribosomal DNA were determined. Phylogenetic analysis using PAUP resulted in five most parsimonious trees. Several larger groups of related genera could be reliably identified. Often the phylogenetic patterns coincide with geographical distribution. The results strongly suggest the paraphyly of the Carduinae. The Centaureinae are most closely related to the large Carduinae genera Jurinea, Saussurea and Cousinia, which are all centred in Central Asia. Within the mainly Mediterranean Carduus-Cirsium complex, genus delimitation is critically addressed.