We evaluated the systematic relationship of the two sections of Raphanus (Brassicaceae) on the basis of morphological and ITS data. We obtained strong support that Raphanus is a polyphyletic group embedded in the Oleracea lineage of the tribe Brassiceae. Section Raphanis, which includes Raphanus raphanistrum, R. pugioniformis and R. sativus, is a strongly supported monophyletic lineage. Section Hesperidopsis is embedded in a different lineage together with Brassica deflexa and B. aucheri. We propose to reinstate the genus Quidproquo in place of Raphanus sect. Hesperidopsis as reflected by both morphological data and ITS phylogeny.