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In Herzegovina, different genotypes of grapevine are called the same, and the origin of these cultivars is mainly unexplored. Two groups of autochthonous cultivars are grown. The first group consists of more widespread Žilavka and Blatina, and accompanying Bena, Krkošija, Dobrogostina and Trnjak, and the second one of less common cultivars that should be preserved from extinction. Considering the small number of studies on the comparison of different methods used for analyses of similarities and relatedness of grapevine germplasm, it was interesting to assess the use of morphological characterization with molecular markers in identification of cultivars in Herzegovina. The results indicate that a similarity coefficient had a broad value range for both methods. Both methods successfully in different ways differentiated all analysed varieties, and for complete and comprehensive identification of grapevine varieties should be use.