Tunisian apricot germplasm consists of two kinds of material: grafted cultivars and seed-propagated Bargougs. A total of 144 accessions were selected for this study, including 109 cultivars accessions and 35 Bargoug accessions. A comparative analysis of the genetic structure was carried out utilizing morphological characters and AFLP molecular markers separately and in combination, with the aim of estimating the genetic diversity and identifying relationships with the geographical origins of the accessions. The hierarchical clustering structure obtained with each dataset revealed that the accessions could be divided into two different genetic groups, indicating two distinct gene pools. This result highlighted the existence of two distinct genetic origins of apricot genotypes in Tunisia. Moreover, Tunisian apricot diversity was classified according to the geographical origins of the accessions, with four regions being distinguished: North, Center, South-East and South-West (Oasis). The perfect accession distribution was based on the four predefined regions, as confirmed by the discriminant analysis. Furthermore, a correspondence analysis revealed a structure in two distinct groups and the existence of accessions from the four predefined regions in each group, which is evidence that Bargougs and grafted cultivars share the same genetic origin. Both markers (morphological and AFLPs markers) were complementary and contributed substantially to the diversity analysis with the best structure obtained from the combined dataset