The genusTeucriumL. is a well-known medicinal plant belonging to Lamiaceae family and Ajugoideae subfamily. The present study aims to evaluate the taxonomic status of theTeucriumspecies using both morphological and flavonoid characteristics and to determine the flavonoid classes. A total of 64 accessions belonged to eight species, and five subspecies were collected from different Zagros regions, Iran. Twenty-nine quantitative and qualitative morphological characters were studied. Extraction of leaf flavonoid was accomplished using a rotary evaporator and MeOH 90%. Identification of the chemotaxonomic position and flavonoid class ofTeucriumspecies was investigated by thin layer chromatography, column chromatography and High Performance Liquid Chromatography-Micromass Quattro micro Atmospheric Pressure Ionization Mass Spectrometer. All information was analyzed using NTSYS pc. 2, PAST v.3.18 and Cluster Vis v. 1.8.2. According to the findings,T. poliumaccessions significantly revealed the highest value of morphological and flavonoid variations. All subspecies ofT. orientalewere definitely separated, but some relationships were observed between its subspecies, includingtayloriandglabrescens. All members of two sections ofPoliumandTeucriswere definitely recognized. A total of seven flavonoid classes were determined from which the highest amounts of abundance were attributed to flavones (18) and isoflavones (17). In conclusion, morphological and flavonoid markers were introduced as appropriate characteristics in the taxonomic relationships ofTeucriumspecies. All the evidence of the present research was first described for Iran.