In the current study, phenotypic and seed-micromorphology variability of 106 accessions from Dactlorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis mascula (L.) L., Orchis simia Lam., Anacamptis coriophora (L.) R.M.Bateman, Pridgeon & M.W.Chase, Ophrys schulzei Bornm. & Fleischm., Ophrys straussii Fleischm. & Bornm., and Orchis collina Sol. ex Russ. species was evaluated. Most of the evaluated traits represented coefficient variations (CV) <30% mainly for economically valuable traits including inflorescence length, flower number, flowering duration, tuber fresh weight, and tuber dry weight. The highest mean value for tuber width (5.61 ± 1.43 cm), tuber length (7.36 ± 1.27 cm), tuber fresh weight (23.38 ± 4.84 g), and tuber dry weight (2.80 ± 0.40 g) was recorded in Ha.JA population belonged to H. affine. The thickest (260.2 ± 1.50 µm) and the thinnest seeds (150.12 ± 9.29 µm) belonged to Os.P population belonged to O. simia and Du.M population belonged to D. umbrosa, respectively. There were highly significant positive or negative correlations between flower, inflorescence, and tuber characteristics. In this regard, the fruit set percentage was positively correlated with flower number (r = 0.36) and flowering date (r = 0.57). Tuber fresh weight was positively correlated with leaf number (r = 0.66), root length (r = 0.77), and root number (r = 0.63). Furthermore, the principal components with eigenvalue more than 0.45 were defined as being significant where eight components explained more than 93.33% of the total variance. The Ward dendrogram based on the Euclidean distance distinguished six distinct groups where accessions within O. collina, H. affine, O. coriophora, and D. umbrosa were placed in I, II, III, and V clusters, respectively. On the other hand, the accessions within O. schulzei and O. straussii formed cluster IV, while the accessions within O. simia and O. mascula were grouped into cluster VI, respectively. Overall, morphological traits at whole plant scale combined with seed-micromorphology characters not only could discriminate and clarify the relationships among the species and their populations collected from geographically different locations but also they could identify the diversity among the accessions within each population and species.