Self-incompatibility is an important way for plants to avoid inbreeding and thus to maintain excellent species. Japanese apricot is a kind of typical gametophyte self-incompatibility (GSI) species. In this study, AS-PCR (Allele Specific PCR) technique and sequencing were used to analyze and identify S-RNase genotypes and SFB genotypes of 11 cultivars. First, primer pairs Pru-C2 and PCE-R, SFB-C1F and Pm-Vb were designed according to the conservative region of the S-RNase gene and SFB gene of Japanese apricot. Then, the genomic DNA was used as a template for AS-PCR amplification and PCR products sequenced directly. After sequences comparison and analysis, the S-RNase genotype and SFB genotype of 11 Japanese apricot cultivars were ‘Ruantiaohongmei’ of S13S14 and F-box2/SFB14, ‘Xiaoyezhugan’ of S3S33 and SFB51/SFB53, ‘Zhonghong’ of S3S24 and SFB2/SFB24, ‘Qingjia915’ of S3S15 and SFB2/SFB43, ‘Meilinhong’ of S1S37 and SFB1/SFB24, ‘Chifenghongmei’ of S14S38 and SFB12/SFB49, ‘Dalongmei’of S20S30 and SFB7/SFB41, ‘Hongguangmei’ of S3S33 and SFB24/SFB55, ‘Nannongfengyu’ of S3S5 and SFB31/SFB43, ‘Nannongfengjiao’ of S3S6 and SFB2/SFB47, ‘Nannonglongxia’ of S15S37 and SFB41/SFB43. Further analysis of the obtained S-RNase gene and SFB gene sequence showed that in addition to the known S-RNase gene and SFB gene, and two unregistered S-RNase genes of S37-RNase and S38-RNase, and five unregistered new SFB genes SFB47, SFB49, SFB51, SFB53 and SFB55 were also identified. Their sequences have been registered in the GenBank database, the accession numbers were MT950061 and MT950062, MW186463, MW186465, MW186467, MW186469 and MW186471, respectively. The research results provide a basis for the allocation of pollination trees for Japanese apricot production and cultivation and the improvement of breeding efficiency.