Self-compatibility has become the primary objective of most almond (Prunus amygdalus Batsch) breeding programmes in order to avoid the problems related to the gametophytic self-incompatibility system present in almond. The progeny of the cross 'Vivot' (S (23) S (fa)) x 'Blanquerna' (S (8) S (fi)) was studied because both cultivars share the same S (f) allele but have a different phenotypic expression: active (S (fa)) in 'Vivot' and inactive (S (fi)) in 'Blanquerna'. In addition, the microscopic observation of pollen tube growth after self-pollination over several years showed an unexpected self-incompatible behaviour in most seedlings of this cross. The genotypes of this progeny showed that the S (fi) pollen from 'Blanquerna' was not able to grow down the pistils of 'Vivot' harbouring the S (fa) allele, confirming the active function of this allele against the inactive form of the same allele, S (fi). As self-compatibility was observed in some S (8) S (23) and S (8) S (fa) individuals of this progeny, the S (f) haplotype may not always be linked to the expression and transmission of self-compatibility in almond, suggesting that a modifier locus may be involved in the mechanism of self-incompatibility in plants.