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Although originally ascribed to the genus Gymnadenia R. Br. (Orchidinae: Orchidaceae), the Balkan endemic orchid G. frivaldii Hampe ex Griseb. has since been more frequently assigned to Pseudorchis Séguier (syn. Leucorchis E. Mey., Bicchia Parl.). Molecular phylogenetic analysis using the ITS region of rDNA reveals a large disparity between the two genera and demonstrates that frivaldii is embedded well within Gymnadenia s.s. Macromorphological and SEM studies further elucidate the floral and vegetative similarities between G. frivaldii and Pseudorchis, notably the heterochronically reduced gynostemium and small, short-spurred labellum; these similarities represent convergent evolutionary transitions, whereas other characters such as contrasting stigma and tuber morphologies provide stronger phylogenetic signals. The sequence-based phylogeny suggests that G. frivaldii represents one of three cases of independent paedomorphic floral reduction inferred in the genus; simplification has been more severe than in G. odoratissima but less severe than in the closely related Gymnadenia subgenus Nigritella. Alternatively, an effectively instantaneous evolutionary origin through hybridisation with a (most likely diploid) species of subgenus Nigritella remains possible. Reports of rare hybridisation between G. frivaldii and members of subgenus Nigritella are acceptably well documented, whereas reports of hybridisation with several other more phylogenetically distant orchid species (including the often sympatric Pseudorchis albida) are considered less secure.