This study addresses the taxonomic relationships and genetic variation of wild Pistacia germplasm in Turkey using morphological data and RAPD analysis. P. atlantica, P. terebinthus and P. eurycarpa are common wild species in the flora of Turkey, and their phenotypic appearance and productivity are highly variable. Understanding such variation would facilitate their use in rootstock breeding programs as rootstock for edible pistachio. We have sampled and characterized a total of 40 wild Pistacia genotypes from different parts of Turkey for this study. These included 10 P. eurycarpa (locally identified as P. khinjuk) genotypes from Siirt and Gaziantep provinces and 20 P. atlantica and 10 P. terebinthus genotypes from Adana, Aydin and Manisa provinces. In addition, two local P. vera varieties, cvs. Kirmizi and Siirt, were added for comparison. Cluster analysis based on morphological data revealed that the closest species to P. vera is P. eurycarpa, followed by P. atlantica and P. terebinthus. Ten polymorphic RAPD primers, yielding a total of 138 scorable bands, were selected and used for DNA fingerprinting of these genotypes. In the resulting molecular phylogeny, the four Pistacia species are clearly separated from each other. P. terebinthus appears to be the most diverged species, and the closest pair of species was found to be P. atlantica and P. eurycarpa. This supported the classification of trees that had been identified by local growers as P. khinjttk, as P. eurycarpa. Comparison of these samples with a reference P khinjuk, obtained from a germplasm collection in the USA, also supported such identification. Several wild genotypes were found to be inter-specific hybrids, and the RAPD patterns revealed their probable origin. Species-specific markers were identified for each of the four species, and these may aid in future classification of new germplasm materials.