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We studied the effects of different environmental conditions on morphological and genetic variations in the Mediterranean geophyte Asphodelus aestivus in Israel. The study included six populations, ranging from mesic Mediterranean to and ecosystems. The results showed important differential morphological traits in one population of the Mediterranean ecosystem (M1). They included longer leaves, longer inflorescences-stalks, and larger number of flower buds than those found among the other populations. We used RAPD analysis to get a genetic profile for all studied populations: 30 loci revealed by the use of 11 primers were studied on 30 plants from each study site. No unique allele was found. Nevertheless, the M1 population was always different from the others in several molecular markers, and even created a different clade on the phylogenetic tree. Abiotic factors were considered to have caused the differentiation of the M1 population. A contingency chi(2) test for heterogeneity of RAPID frequencies across all locations revealed significant differences in 17 RAPD loci (57%). The estimated genetic diversity within populations was 0.287 according to Nei’s gene diversity and 0.432 according to Shannon’s genetic diversity index. Differentiation among six populations of the RAPD loci (G(ST)) ranged from 0.014 to 0.354 with a mean of 0.096. Principal coordinate analysis indicated the presence of genetically distinct sub-regional groups. Genetic and geographical distances among A. aestivus populations along the environmental gradient were found to be correlated, with the exception of the M1 population. In the present study, levels of gene variability within populations were higher than those between populations. Nevertheless, if we discard the unique M1 population, a clear genetic pattern linked to aridity and geographical distance was discerned.