In Central Europe, the genus Platanthera traditionally comprised two species, P. chlorantha Cust. ex Rchb. (Pc) and P. bifolia (L.) Rich. (Pb). They are morphologically characterized by a wide and narrow separation of anthers, respectively. However, a third form with intermediate anther distance has repeatedly been hypothesized but only hesitantly accepted. In addition, intermediate morphology has been also used as the main character of P. x hybrida. However, the status of some purported hybrid populations is challenged by the local lack of parental species, their successful reproduction and non-intermediate traits. Despite this unclear situation, detailed genetic and morphological analyses are lacking. Here, we studied morphology and molecular markers within the P. chlorantha/bifolia group in Central Europe. Three morphological groups emerged representing Pc, Pb and a third form, here informally referred to as non-hybrid intermediates (Pn). The latter is characterized, among other trait differences, by intermediate distance between anthers [(0.7)-1-2.2 mm] and long spurs (28-40 mm). Three gene pools were identified, which largely corresponded to the three morphological groups. The Pn gene pool had several high-frequency private alleles substantiating its genetic independence. Some of the Pn populations were previously interpreted as P. x hybrida suggesting that Pn was overlooked hitherto and mistaken to represent hybrids. The non-perfect fit between morphological and genetic groups highlights the potential for fast morphological evolution. Overall, the finding of three distinct lineages within the bifolia/chlorantha group necessitates a thorough reanalysis of reported taxa and a reevaluation of our understanding of their distribution, ecology and evolution.