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Amplified fragment length polymorphism and inter simple sequence repeat markers were used to assess the genetic structure of Cistus ladanifer and its genetic differentiation from co‐occurring Cistus species. Clear genetic differentiation was found between two populations corresponding to the morphological description of Cistus palhinhae and the 23 Cistus ladanifer populations analyzed. However, the magnitude of differentiation (DICE coefficients >0.98) appears to be more in agreement with the taxonomic designation of Cistus ladanifer ssp. sulcatus, which has been proposed by some authors, and not C. palhinhae. Dendrogram analysis of the genetic relationships among Cistus ladanifer, Cistus populifolius, Cistus monspeliensis, Cistus crispus, Cistus libanotis, Cistus salvifolius and Cistus albidus, with Halimium halimifolium as an outgroup, showed two main clusters. Taxa composition of these clusters …