Seedless berberis is one of the few crops which are cultured only in Iran and south khorasan. However, there has been no effort in the field of identification, polymorphism evaluation and study of genetic structure of seedless Berberis populations and its relative existing in Iran. In addition, despite the classical studies made based on botany and systematics around the world, there are still ambiguities and debates about the phylogenetic relationships within species existing in this family, mainly due to different efficiency. of different methods. So in this paper- for the first time in Iran morphological markers were used to evaluate variation and phylogenetic relationships among Berberis populations of khorasan provinces 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. Since experimented morphological traits comprise about 90% of the traits existing in identification key of Flora Iranica and are often vegetative, week evaluation and correlation between AFLP data and morphological markers based on identification key 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 spieces and genera of Berberis family looks necessary.

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