Apricot (Prunus armeniaca L.) exhibits a gametophytic self-incompatibility (GSI) system and is mostly considered to be a self-incompatible species though numerous self-compatible exceptions occur. A set of 68 local Tunisian apricot accessions coming from different geographic areas was examined by PCR analysis of the S-loci genotypes. Up to nine S-alleles were detected within the Tunisian apricot germplasm allocating the studied accessions into 14 cross-incompatibility groups, nine of them newly identified in this study. Self-compatible accessions carrying the SC-allele were revealed for the first time within the Tunisian apricot germplasm. The heterogeneous distribution of the apricot S-alleles confirmed the species’ domestication and diffusion history from the Irano-Caucasian region to North-Africa. The knowledge of incompatibility relationships among apricot accessions can be a highly valuable tool for the development of future breeding programs by selecting the appropriate parents and for efficient orchard design by planting a combination of self-compatible and inter-compatible accessions.