Gymnadenia densiflora was recently either misinterpreted or not accepted as a distinct taxon by several authors. To resolve its taxonomic position and differentiation from the related G. conopsea, a detailed study of the morphology, chromosome numbers and distribution of these two taxa in the Czech Republic, Slovakia and neighbouring areas was carried out. Chromosome counts showed an invariable diploid chromosome number (2n = 40) for G. densiflora, while G. conopsea is diploid, tetraploid and rarely also pentaploid (2n = 40, 80, 100). Results of morphometric analyses (principal component analysis, cluster analysis, classificatory and canonical discriminant analysis) confirmed a good morphological separation between G. densiflora and G. conopsea. Characters such as the width of the second lowermost leaf, height of the plant, number of flowers in the inflorescence, number of leaves, and the ratio of height of the plant and distance from the stem base to the base of the uppermost sheathed leaf contributed most to this separation. Our study supports the recognition of G. densiflora as a distinct species.