Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae).

•RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may explain discordant tree topologies.•An origin of Gymnigritella runei from extant G. conopsea and N. nigra is supported.•The separation of G. densiflora from G. conopsea s.str. is supported.•Affiliation of Nigritella polyploid taxa into three distinct groups is supported.