Studies on the phylogeny of the genus Pistacia are rather few, and mostly based on morphological characterization. P. palaestina had been described morphologically either as a different species or as a variety of P. terebinthus. In this study, we perform the molecular characterization of P. palaestina, within the study of phylogenetic relationships among nine Pistacia species by RAPD analysis. Parsimony analysis showed that the closest pairs of species were P. terebinthus and P. palaestina, and we suggest that P. palaestina is, in fact, a variety of P. terebinthus in view of the small genetic distance between them. To confirm this hypothesis, we analysed two additional P. terebinthus and two additional P. palaestina samples (from Israel and Turkey) using the same primers obtaining similar patterns. The results show that leaf characters probably are not sufficient to consider P. palaestina as a different species. Therefore, we propose to consider P. palaestina as a variety of P. terebinthus.