A group of Lamiaceae that has caused confusion over its generic boundaries are those species belonging to the complex surrounding the genera Satureja, Calamintha, Micromeria, Clinopodium and Acinos. In the current study, morphological and taxonomical characteristics of two endemic subspecies of Clinopodium troodi (Post) Govaerts subsp. vardaranum (Leblebici) Govaerts and Clinopodium troodi (Post) Govaerts subsp. grandiflorum (Hartvig and A.Strid) Govaerts were studied for the first time using stereoscopic microscopy and detailed descriptions and illustrations of general appearance of plants and their leaf, bract, flower, calyx, corolla and fruit shapes were described and illustrated. At the same time, the variation borders of subspecies in Flora of Turkey was expanded and a identification key prepared. According to Flora of Turkey, status of a sample collecting from Denizli of C. troodi is doubtfull and here its real status was determined as subsp. grandiflorum.