Almonds are self incompatible, the incompatibility being controlled by a multi allelic (S-alleles) single gene. The incompatibility alleles were studied in 96 samples of wild almonds and related Prunus species from 10 taxonomic groups. Polymerase Chain Reactions were carried out with six primer sets including: three degenerate primer pairs (PaConsI-F(FAM)/EM-PC1consRD, PaConsI-F(FAM)/EM-PC3consRD, EM-PC2consFD/EM-PC3consRD), one primer pair (AS1II/AmyC5R), one allele specific primers pair (CEBASf/AmyC5R), and a set of multiplex primer (AS1II/CEBASf/AmyC5R). The number of amplified bands (155) as well as their size ranges were recorded as higher than those in the previous reports. None of the primer sets amplified self compatibility allele (Sf). The sizes of amplified alleles compared with previous reports in almond cultivars, and the alleles were labeled accordingly. Alleles S9, S2, S13, and S25 had highest frequencies (12.26, 8.39, 7.74 and 7.74 respectively). Alleles S16, S17, S18, S19, S22, and S28 were not observed, and while S15 S26 were of the lowest frequency (0.65) in the studied samples. Presumably, geographical distribution of these species had influenced their S-allele frequencies. The putative groups were clustered by using amplified allele sizes from the first degenerate primers (PaConsI-F(FAM)/EM-PC1consRD). This clustering was in match with botanical classification.