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We assessed the genetic differentiation of the Mediterranean olive from its wild relatives found in different geographic areas (Mediterranean, Asia, Africa) using eighty RAPDs revealed with eight primers. Variance analysis (AMOVA) enabled us to estimate the overall genetic differentiation parameters between wild populations. Oleasters from the Near East and Turkey were discriminated from the other Mediterranean populations. Olea laperrinei, O. maroccana and O. cerasiformis were the taxa the most related to the Mediterranean olive. In contrast, O. africana was shown to be the most genetically distant taxa from the Mediterranean olive. However, we characterised hybrid trees between these two taxa. Significant trends between genetic and geographic distances were met within the subspecies cuspidata and within the Mediterranean olive. A genetic diversity gradient was observed in both subspecies europaea and cuspidata. These results are in agreement with a mechanism of differentiation by distance in the O. europaea complex, but another non-exclusive mechanism could also be gene flow between differentiated taxa. Furthermore, we characterised the discriminating power of each RAPD to recognise the different taxa using intraclass correlation coefficients. Lastly, IGS-RFLPs enabled us to assess rDNA polymorphisms on a sub-sample of individuals. On the basis of these data, a low interspecifc differentiation was found. This suggests a recent genetic divergence between the different taxa of the O. europaea complex or the occurrence of gene flow during favourable periods or because human displacements. All the olive cultivars were genetically related to the oleaster populations supporting that Mediterranean is the olive domestication area.