Almond (Prunus dulcis Mill.) has numerous S-alleles and therefore many combinations of incompatibility groups. The identification of these groups is important for designing crossing matrices for breeding, selecting progeny and testing for hybridity. This work describes a novel molecular technique for the identification of S-alleles in almond using PCR primers designed from the sequences of the introns without the need for restriction enzyme digestion. Thirteen specific pairs of primers have been designed for the S1, S2, S3, S4, S5, S6, S7, S8, S9, S10 (putative), S11, S23, and Sf alleles. The S23 allele has been detected in some old South Australian almond selections, and is possibly derived from an early importation of the cultivar 'Ramillete' from Spain. This technique provides a quick and precise method for predicting incompatibility alleles from the genomic DNA of almond cultivars. The practical use of this new technique in the Australian almond breeding programme is presented here.