Samples of Capparis spinosa plant were collected from 6 sites in Aleppo and Lattakia provinces. The genetic variations were studied using the AFLP technique in order to determine the genotypes of the studied types using 3 primers, which showed amplification. Statistical analyses were conducted using the dissimilarity coefficient and genetic diversity coefficient. The A.C.P. and the statistical -F were calculated, and the similarity dendrogram was constructed. The results showed the following: The presence of a certain number of specific alleles (descriminates) for each province. The presence of genetic and reproductive isolation deterrent to gene flow between the two provinces. The heterozygoty average was a little higher in Lattakia (0.486) than in Aleppo (0.481). The mean of genetic diversity coefficient of primers and individuals was a little higher in Aleppo (0.677) than in Lattakia (0.653). The population mean was very close: (0.759) in Aleppo and (0.760) in Lattakia. This may be explained on the basis of silent and specific alleles due to deletion mutations, different selective effects as well as the reproduction system in the two cities. The greatest genetic distance in Aleppo was (0.381) noted between (Al Dahea and Al Shekh saaed), and in Lattakia (0.38) noted between (Al Amroniah and Jabla). However, the greatest genetic similarity in Aleppo was (0.637) noted between (Al Shekh Saaed and Turkman Bareh), and in Lattakia (0.675) noted between (Wata Deirzenon and Jabla). The variation between these values was graduated. The study of statistical –F showed the effect of the similarity factor in some populations. This was more significant in Aleppo than in Lattakia, which indicates that the reproduction system is more closed in Aleppo, and this refers as well to inbreeding or self pollination which showed high genetic variations in these populations when compared with Lattakia. The results of this study helped in determining primers that can be used as molecular markers in a breeding program for Capparis spinosa as a medicinal plant. This technique showed high efficiency in studying the similarity relationships between these two cities.