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In this study, the phylogeny and morphological variation of 6 species of the genus Cousinia sect. Stenocephalae, i.e., C. hypopolia, C. decipiens, C. esfandiarii, C. renominata, C. stahliana and C. daryoushiana, distributed in NE regions of Iran, were investigated. ITS, ETS and rpl32-trnL ^(UAG) sequences for 12 species (17 specimens) were generated. Phylogenetic interspecies relationships were constructed by Bayesian method and likelihood analysis. The specimens were also investigated in terms of morphological characters. Despite very similar morphological characters and geographical distributions, the separation of these species was confirmed by the obtained results of the molecular data (combined data of plastid and nuclear sequences). On the basis of the present study, the above-mentioned species were almost separated from each other by morphological characters and molecular data. A diagnostic key and the description of these species were also presented. These results did not conform with the previous palynological and anatomical studies of the species.