Tunisian apricot genetic resources, formerly cultivated in different geographical areas of the country in the North (Testour and Ras Jbel), the Centre (Kairouan, Sfax, Mahdia) and the South (Gabes, Mareth, Jerba, Gafsa, Midess), cover different climatic conditions ranging from the sub-humid (North) to the arid (South) areas. Their phenotypic diversity is rather large, even if only a few cultivars are of market interest. For this reason, apricot landraces are threatened by severe genetic erosion. To face the problem and preserve the existing biodiversity, actions have been carried on and 48 distinct cultivars have been identitied and characterized on morphological and molecular bases. The present study deals with the comparative analysis of the characterization data sets including the relationship between molecular markers and morphological traits, and with the assessment of the phylogenetic structure of the related cultivars with regard to their geographical origin. Morphological charactterization has been assessed using 28 qualitative characters according to the UPOV descriptor and 13 quantitative morphometric parameters. AFLP molecular markers were investigated using 7 primer combinations: 268 polymorphic bands were registered suggesting a high level of polymorphism. High genetic diversity is revealed among the Tunisian apricot cultivars. The 48 cultivars were distinguishable either by morphological or by molecular bases. They were structured into two groups genetically related to two main introductions of apricot in Tunisia. Diversity structure seems to be correlated to tbe geographical distribution of the accessions where the three Northern, Central and Southern regions are clearly distinguished.