Using DNA barcoding markers, we inferred the phylogenetic relationships of the genus Anacyclus including for the first time the three Eastern Mediterranean species, A. anatolicus, A. latealatus and A. nigellifolius. Our results conclusively reveal the polyphyletic condition of this genus in its current circumscription. The molecular data show that A. anatolicus, A. latealatus and A. nigellifolius do not belong to Anacyclus. According to the current knowledge of the Anthemideae systematics, these three species should be placed within the genus Cota and thus the new combinations Cota anatolica, Cota latealata, and Cota nigellifolia are proposed. Such a taxonomic placement is congruent with the achene morphology and biogeography although the circumscription of Cota itself requires further studies.