The California almond industry is the largest supplier of almonds [Prunus dulcis (Miller) D.A. Webb] in the United States and throughout the world. Self-incompatibility is a major issue in almond production as it greatly affects nut set. In this study, we determined full-length sequences for alleles Sa - Si, determined the genotypes of 44 California cultivars, and assigned the cultivars to cross-incompatibility groups (CIGs). Newly identified S-alleles led to an increase in the number of CIGs. A pairwise distance tree was constructed using the aligned amino acid sequences showing their similarity. Four pairs of alleles (Sc and Se, Sg and Sh, Sd and Sj, and Sb and Sf) showed high sequence similarity. Because of its simplicity, reproducibility, and ease of analysis, PCR is the preferred method for genotyping S-alleles.