In the present study, a total of 20 cultivars of apple (Malus x domestica Borkh.) were characterized for their S-alleles using ten allele specific PCR primers. 13 cultivars were assayed for the very first time while 7 were validated and re-confirmed. The cultivars were selected on the basis of their characteristics of enhanced shelf life, improved aroma, attractive color, crispy flesh and resistance to scab and other diseases, which could essentially be a prime reason for their incorporation in various breeding programmes, for transmission of traits of desirability into the progenies. Amplification parameters were standardized for each PCR primer using 7 positive control samples. We reported 14 diploid cultivars, 2 triploids while only single S allele was observed in 4 cultivars. Frequency analysis reported highest diversity of allele S9, followed by S3 > S2,S0,S28 > S1 > S5 > S7,S23. S24 was found to be completely absent in the evaluated cultivars. Consequently, three incompatibility groups were framed based on the S genotype of these cultivars, which comprised of 2 completely incompatible crosses, 76 partially compatible combinations whereas, 106 completely compatible pollination combinations were reported in the study. We formulated another incompatibility group amongst 4 partially genotyped cultivars comprising of 6 possible cross combinations which may be confirmed upon their complete S allele characterization. The compilation shall be helpful for future breeding programmes, for confirmation of hybrids of a cultivar and for proper orchard planning. The study would further help in effectively reducing the time required for hybridization, by eliminating the completely incompatible parental crosses beforehand.