The olive tree was primary domesticated in the North-East Levant at least six millennia ago. Nowadays monumental trees are surviving across the Mediterranean Basin. These ancient, traditional varieties testify for the long cultivation of the crop but this germplasm remains incompletely characterized. Here, we investigated the genetic diversity among Lebanese cultivated olives in comparison to accessions from the whole Mediterranean Basin. Seventy-three olive trees including six monumentals were sampled in four main Lebanese areas, and characterized with 12 nuclear microsatellites and 39 plastid DNA markers. These genetic profiles were combined to those previously obtained in the world collection of Marrakech (WOGB) and analyzed with a phenetic approach, a multivariate analysis, and a Bayesian clustering method. Three main genetic clusters were identified in the Mediterranean cultivated olive tree as previously shown. The majority of Lebanese olive trees were assigned to the Eastern Mediterranean gene pool. A few genotypes were however assigned to the Central Mediterranean cluster. Plastid DNA markers revealed the presence of four haplotypes belonging to lineages E1 (72 olive trees) and E2 (one plant). Haplotype E1.1 that originated in the Eastern Mediterranean was found in 68 individuals (93 %). Within the common variety "Baladi", several nuclear microsatellite profiles were identified including closely related olive trees that may correspond to molecular variants due to somatic variation. The six monumentals were remarkably positioned close to the Cypriot accessions and showed three different profiles, one of which matched to the most common profile of the widespread traditional variety "Baladi". Our findings suggest that the Lebanese olive trees were locally selected during the beginning stages of olive growing and served as basic plant material for the current traditional varieties derived by both sexual and clonal propagation. Recent variety introductions from westernmost regions were also evidenced, but only in modern orchards from the Bekaa district.