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Systematic and evolutionary relationships within the diploid Western Mediterranean Phlomis crinita/lychnitis complex remain controversial apparently due to hybridization and introgression. This study examines patterns of sequence variation in the nuclear ribosomal DNA (ITS region) and three non‐coding plastid DNA regions (trnH‐psbA, trnT‐trnL and atpB‐rbcL) in this complex in an aim to clarify whether hybridization, introgression or lineage sorting resulting from recent diversification is mainly responsible for poorly understood relationships. Information recovered from nuclear and chloroplast markers was found to be strongly incongruent. Phylogenetic analysis of inferred nuclear ITS ribotypes is consistent with previous morphometric and taxonomic results in distinguishing two sister lineages, P. crinita s.l. and P. lychnitis. In addition, the high number of additive polymorphisms detected in ITS sequences suggests …