In this study, important morphological traits and self-incompatibilities in 71 almond cultivars and genotypes were studied. Simple and multiplex specific PCR analyses were used to identify self-incompatibility alleles. Based on the results, cultivars and genotypes, including ‘Dir Ras-e-Savojbolagh’, ‘D-124’, ‘D-99’, ‘Shahrood 12’, ‘Tuono’, ‘Nonpareil’, ‘Price’, ‘Mirpanj-e-Tehran’, ‘Pakotahe-e-Taleghan’, ‘V-13-34’, ‘V-16-8, ‘V-11-10’, ‘Zarghan 10’, ‘Uromiyeh 68’, ‘Barg dorosht-e-Hamedan’ and ‘Yazd 60’ were late flowering and had the highest quality nut and kernel characters. The result of the PCR method using combined primers AS1II and AmyC5R showed amplification of ten self-incompatibility alleles (S1, S2, S3, S5, S6, S7, S8, S10, S12, and unknown allele) and three Sf alleles. Moreover, S1 had the highest frequencies in comparison with other known S-alleles. Some native genotypes such as ‘D-124’ and ‘D-99’were the best trees in terms of nut and kernel characters. Also, unknown alleles with different sizes of PCR products were detected and 58 new bands were found in some cultivars.
