Centaurium bianoris (Gentianaceae) is restricted to Majorca, the main island of the Balearic Archipelago. This tetraploid species is characterised by salmon-coloured corollas (var. bianoris), but pink (var. roseum) and yellow (var. sulfureum) varieties have also been described. An allopolyploid origin has been proposed between the diploids C. maritimum (yellow flowers) and C. tenuiflorum var. acutiflorum (pink flowers), both occurring on Majorca and in other places of the Mediterranean basin. In this study, we tested the proposed hybrid origin of C. bianoris by using RAPD fingerprinting, and both direct and cloned sequences of the nuclear ribosomal ITS, and the chloroplast trnLF regions. Our molecular data confirmed the hypothesis of an allotetraploid origin of C. bianoris via hybridisation between C. tenuiflorum and C. maritimum, the latter being the maternal parent. The so-called varieties roseum and sulfureum appeared to be only floral morphs that may have arisen via genomic processes such as gene silencing. Hybridisation is probably the cause of the ITS sequence polymorphism observed in C. bianoris, whereas backcrosses with either parent may be responsible for the apparent bidirectional homogenisation observed in ITS clones. Finally, the polyphyletic behaviour of C. bianoris on the ITS cladogram, combined with the differential rates of homogenisation observed in ITS sequences, may denote a recurrent origin for that taxon. This result contrasts with the narrow distribution of C. bianoris, compared to that of its diploid parents, suggesting instead a single origin for this hybrid.