We aimed to describe and analyse the morphological, anatomical and micromorphological traits of 36 Turkish orchids representing 12 genera (e.g. Anacamptis, Cephalanthera, Dactylorhiza, Orchis, Serapias) in detail and analyse their usability for solving phylogenetic and taxonomic issues. We applied UPGMA cluster analysis to anatomical, morphological and micromorphological characters such as root tubers, leaf and flower structures, pit, sclerenchymatic sheath, vascular bundle shape, crystal and starch, exodermis and endodermis structure, stomata type, bulliform cells in roots, shoots and leaves, surface structures like papillae, hairs and ornamentation on flower parts, leaves, fruits and seeds. Furthermore, in a phylogenetic framework, we analysed nuclear ribosomal ITS diversity in the same orchid species belonging, and in a combined Bayesian phylogenetic analysis based on anatomical, morphological, micromorphogical and ITS data we confirmed the usefulness of multiple data sets for effectively assessing taxonomically critical orchids. In the combined analysis, all genera were resolved as monophyletic with topologies congruent with recently published more thorough molecular phylogenetic reconstructions, while the trees obtained by seprately analysing the ITS and the anatomical, morphological, micromorphogical data were less resolved and partly inconclusive.