S-4' is a pollen-part mutant in sweet cherry (Prunus avium L.) that is extensively used to develop self-compatible cultivars. The S-4'-haplotype is known to have a functional stylar component and a nonfunctional pollen component. The pollen component in sweet cherry necessary for the specificity of the pollen reaction is believed to be an S-haplotype specific F-box protein gene, called SFB. This study describes two molecular markers that distinguish between SFB4 and SFB4' by taking advantage of a four base pair deletion in the mutant allele. The resulting polymerase chain reaction (PCR) products can either be separated directly on a polyacrylamide gel or they can be subjected to restriction enzyme digestion and the different sized products can be visualized on an agarose gel. The latter technique utilizes restriction sites created in the PCR products from the SFB4' allele, but not the SFB4 allele. Because the primer sets created differential restriction sites, these primer sets were termed dCAPS (derived cleaved amplified polymorphism sequence) markers. These molecular assays can be used to verify self-compatibility conferred by the S-4-haplotype.