The genus Anthemis has a circum-Mediterranean distribution and comprises c. 175 annual, biennial, and perennial species with polyploid species and species complexes found in its section A. sect. Hiorthia. In Sicily, the genus is represented by 13 species, one of these being the tetraploid A. cupaniana, which is endemic to the island and is distributed throughout the limestone mountains at elevations between 500 and 1800 m a.s.l. Discordant positions in phylogenetic trees based on two plastid regions (psbA-trnH and trnC-petN) and on one nuclear marker (nrDNA ITS1 + 5.8S + ITS2) reveal that the species is of allopolyploid origin, with the maternal parent from the species group around A. cretica and the paternal one from a monophyletic group comprising mostly N African representatives around A. pedunculata. Owing to the fact that the latter group also comprises the Sicilian perennial and diploid A. ismelia and that A. cretica has been found with diploid populations in the C Sicilian Madonie Mts, these two species are considered being the most probable parental diploids of A. cupaniana. The close relationship of A. ismelia with the N African A. pedunculata group supports the biogeographical interpretation of A. cupaniana being the result of a 'collision' between diploids from the southern (African) and northern (Eurasian) platforms after dispersal along a Pleistocene corridor in the Sicilian channel.