Polyploidy and hybridization often provide genetic and phenotypic variability upon which evolutionary forces can act and are therefore considered as fundamental evolutionary processes for diversification in vascular plants, resulting in plant adaptation to changing environmental conditions. However, polyploid speciation is a complex process, potentially involving ecological divergence between lineages of different ploidies and/or genetic mixing with parental species. In the present study, we investigated the origins and dynamics of the Sicilian endemic orchid Neotinea commutata and its relationships with putative parental species. Molecular, cytogenetic and morphometric analyses revealed that N. commutata is a tetraploid derived from hybridization between N. tridentata and N. lactea. However, we also found variation in chromosome number and genome content within N. commutata, indicating that other events, including the possible replacement of the diploid progenitor N. tridentata by N. commutata, may have contributed, or still be contributing, to the evolutionary dynamics of this neoendemic taxon, which appears to be partially reproductively isolated from its progenitors. Distributional data indicate that the allopolyploid N. commutata has been able to establish and spread on the island when compared with its putative parents. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 707–720.