Phoenix theophrasti is one of the few tree species tertiary relict endemic to the eastern Mediterranean, and it is one of the two palm species native to continental Europe. It has local populations both in Crete-Greece and in southwest Turkey. Like most of the relict endemics, it has a restricted distribution and it is at risk of extinction. The primary goal of this study was the genetic characterization of Turkish P. theophrasti populations by using SSR markers. The secondary goal was to detect the phylogenetic relations of P. theophrasti with nine different palm species which are P. dactylifera, P. reclinata, P. rupicola, P. roebelenii, P. canariensis, P. loureiri, P. acaulis, P. sylvestris from Phoenix genus and Chamaerops humilis from Chamaerops genus by the same markers. Chamaerops humilis was included in the study as the second natural palm species of the Europe. The genetic differentiation coefficient (F_ST) was found as 0.34, and the level of gene flow (N_m) within a generation among populations was found as 0.49. In general, excess of homozygotes relative to that expected with random mating was detected in the populations. The lowest differentiation of P. theophrasti was from P. dactylifera (F_ST = 0.1932), and the highest differentiation of P. theophrasti was from C. humilis (F_ST= 0.4261). We propose that P. theophrasti must urgently be included in the Red List of IUCN under the critically endangered (CR) category. Phylogenetic relations determined among the palm species indicated the necessity of re-evaluation of the taxonomy of palms.