Gametophytic self-incompatibility of almond (Prunus dulcis M) controlled by a single locus with several allelic variants. In this study, the S-alleles of 16 Iranian and 6 foreign almond cultivars were investigated by single and multiplex PCR technique with different set of oligonucleotide primers. Application of AS1II and AmyC5R primers with single PCR resulted in amplification of 9 known self-incompatibility alleles S1, S2, S3, S5/10, S7, S9, S11, S12, and S13. Four bands with different sizes from PCR products of known S-alleles were detected in Iranian almond cultivars (Mamaei, Raby, Sahand, Shirbadam, Hajmirzaei and Khorshidi) which may be related to new S-alleles. Multiplex PCR using the AS1II, AmyC5R and CEBASF primers verified the results of single PCR. Furthermore, it was also able to identify Sf-allele in self-compatible cultivars such as Tuono, Genco and Falsa Barese. From 32 S-alleles in Iranian almond cultivars only 28 were identified by using these primers. Two S-alleles for 12 cultivars and one S-allele for four cultivars were identified. S2, S7, S13, S3 and S10 alleles were more frequent than others in Iranian almond cultivars. This technique provides a precise and rapid method for identifying S-alleles from the genomic DNAs of almond cultivars.