This study focuses on molecular phylogenetic investigation of 9 Iranian species of the genus Cyperus. We sequenced alleles from the matK gene. Results obtained from the molecular data indicated that there is no phylogenetic boundary between four species C. rotundus, C. longus, C. digitatus and C. esculentus. Cyperus involucratus and C. alternifolius are grouped in a clade and it is congruent with their morphological similarities. Similarly, C. luzulae and C. eragrostis forms a clade sister to two latter species.

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