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Drought-responsive genes may differ in structure and complexity in native populations of a species established in different ecosystems. Peripheral populations may be a source of genetic variability for breeding cultivated plants for abiotic stresses tolerance and the target for core collections in germplasm preservation programs. Genetic studies including both peripheral and central populations are still limited. This research evaluated genetic diversity of drought-responsive genes in peripheral and central populations of Trifolium purpureum Loisel. Genomic DNA isolated from leaves of three northern and three southern populations of Israel was digested with restriction enzymes and hybridized with four drought-induced and four drought repressed gene fragments. RFLPs were analyzed for gene diversity, molecular variation and fixation indexes (F-ST). Gene diversity of drought-induced genes ranged from 0.1 to 0.42 but differences of individual or pooled genes between central and peripheral populations were nonsignificant. Gene diversity for drought-repressed genes ranged from 0.08 to 0.348. Even though there were no differences for individual genes, a joint analysis showed a significantly larger (P < 0.05). gene diversity in peripheral populations of T Purpureum than in central ones. Variation within populations for both drought-induced and drought-repressed genes was the main component of molecular variance. Fixation index (F-ST) for drought-induced genes was between 0.029 and 0.214 while for drought repressed genes it was between 0.04 and 0.33. Results of this study show that peripheral population might be a reservoir for drought responsive genes.