Thirteen species of Trifolium L. were tested by twenty different 10 mers RAPD primers. The results of the technique RAPD showed clear genetic variations among the species under study and the species were divided into two general groups at the level of similarity 1.42, while taking group I about 11 species, II was isolated with two species T. dasynrum and T. pilulare, the group I it was divided into branches A which separated from the rest of the species T. leucanthum and B which branched into B1 and B2, the B1 included 7 species, while B2 contained three species. The objective of this study was to determine Trifolium 's molecular phylogenesis based on the RAPD method as a genetic taxonomic tool to isolate and separate species.