Although self-incompatibility (SI) in Rosaceae has been considered a single-locus qualitative trait, the evidence observed in different Prunus species has indicated the presence of modifier genes located outside the S locus. The almond progeny from the cross 'Vivot' × 'Blanquerna' has shown an unexpected self-incompatible behavior in most of the seedlings, thus requiring further study. Both parents possess the Sf allele, but with different phenotypic expressions. The male parent is self-compatible with the inactive Sf haplotype and the female parent is self-incompatible with the active Sf allele. Thus, the presence of other factors or genes involved in the mechanism of self-incompatibility in almond could explain the unexpected results. The use of microsatellite markers in this progeny has allowed identification of several loci involved in the SI reaction and to locate these modifier genes in the ‘V×B’ map. These results may indicate that almond is a species with a genetic background of pseudo-self-compatibility controlled by modifier genes.