Summary• In China, its centre of origin, apricot ( Prunus armeniaca ) is self-incompatible. However, most European cultivars are self-compatible. In most cases, selfcompatibility is a result of a loss-of-function mutation within the pollen gene ( SFB ) in the S C haplotype. Controlled pollinations performed in this work revealed that the cross 'Ceglédi óriás' ( S 8 S 9 ) × 'Ceglédi arany' ( S C S 9 ) set well, as expected, but the reciprocal cross did not.• Apricot S 8 , S 9 and S C haplotypes were analysed using a multilevel approach including fruit set evaluation, pollen tube growth analysis, RNase activity assays, polymerase chain reaction (PCR) analysis and DNA sequencing of the S-RNase and SFB alleles.• SFB 8 was revealed to be the first known progenitor allele of a naturally occurring self-compatibility allele in Prunus , and consequently S C = . The first intron of S C -RNase is a phase one intron, indicating its more recent evolutionary origin compared with the second intron. Sequence analysis of different cultivars revealed that more single nucleotide polymorphisms accumulated in S C -RNase than in SFB C . New methods were designed to allow high-throughput analysis of S genotypes of apricot cultivars and selections.• S-RNase sequence data from various sources helped to elucidate the putative origin and dissemination of self-compatibility in apricot conferred by the S C haplotype.