In this study, the sexual incompatibility of Paviot and Levent apricot parents and 89 F-1 (Paviot x Levent) progenies was determined by self-pollination experiments and S-allele-specific polymerase chain reaction (PCR) technique. According to the self-pollination and isolation analyses under field conditions, it was found that the Paviot genotype is self-compatible (SC), whereas the Levent genotype is self-incompatible (SI). It was determined that, of all the progenies, 55 had a fruit set below 5% and were self-incompatible, whereas 34 had a fruit set over 5% and were self-compatible. The PCR-based techniques showed that, in parallel to the data obtained from the field studies, 55 F-1 progenies did not have S-c allele, whereas 34 progenies involved S-c allele. There were ScS2 alleles in the Paviot genotype and S20S52 alleles in the Levent genotype. It was determined that there were S2S20, S2S52, ScS20, and ScS52 alleles in 89 F-1 progenies and the distribution of the four alleles in the progenies was found to be as follows: 35.9% S2S20, 25.8% S2S52, 23.6% ScS20, and 14.6% ScS52. F-1 progenies nos. 41, 46, 86, and 89 should be used as pollinators in further breeding studies.