Abstract Seedless barberry (Berberis vulgaris L. var. asperma) is one of the few crops that is cultured only in eastern parts of Iran. The Origin of this variety is unknown and there has not been any study aiming to identify phylogenic relationships of this plant with other species existing in Iran. In this study, AFLP markers based on four primer combinations (EcoRI/Tru1I) were used to evaluate genetic variation and phylogenic relationship among wild and cultured barberry belonging to north east and eastern Iran, together with 2 species of ornamental barberry and one sample Mahonia aquifolium. Data resulted from cluster analysis, showed that these two genera (Berberis and Mahonia) form 2 completely distinct groups with a significant genetic distance. These results can clarify the ambiguity of separation procedure between Mahonia and Berberis genera. Heterozygosity index, Principal co-ordinates analysis (PCoA), Fst Index and analysis of molecular variance (AMOVA) revealed significant difference among wild barberry populations; so that, as was expected, observed variation within cultured barberry population was very low and near zero. Moreover, Morphological markers were used to evaluate variation and phylogenetic relationships among Berberis populations of eastern Iran compared to data resulted from AFLP markers by means of Mantel correspondence test. The results showed that there is a low correlation between AFLP data and morphological markers. These results can indicate low efficiency of identification key of Flora Iranica for classification and phylogenetic consideration of Berberis family. Therefore further molecular and morphological investigations aiming better understanding of the relationships between species and genera of Berberis family looks necessary.

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