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The genetic variation of six Tunisian Myrtus communis L. (Myrtaceae) populations was assessed using nine isozymes coding for 17 putative loci and 79 RAPD markers, amplified by five decamer random primers. The analysed populations belonged to three bioclimatic zones (lower humid, sub-humid and upper semi-arid). A high genetic diversity within populations was detected both by isozymes and RAPDs. The level of variation differed according to bioclimate. Populations collected from sub-humid bioclimate showed more polymorphism than those grown in the upper semi-arid zone. For all populations, the genetic diversity revealed by RAPDs was more pronounced than that detected with isozymes. A high differentiation among populations related to bioclimate and geographic distance was revealed by both methods. Population’s structure based on RAPD markers was more concordant with bioclimatic zones in comparison with isozymes. Differentiation between ecological groups was higher than that revealed within groups. Conservation programs should take into account the level of genetic diversity within population revealed by the two complementary classes of markers according to bioclimate.