Abstract: Apples (Malus ×domestica Borkh.) are one of the largest economically signiﬁcant fruit crop worldwide. Due to the self-incompatibility of most Malus cultivars, the apple industry relies on insect pollinators to aid in cross-pollination to improve seed and fruit set. The introduction of crabapples as pollinizers has become a popular practice to promote cross-pollination in commercial apple orchards. Genetic compatibility with a desired apple cultivar is a critical feature of eﬀective pollinizers, but the S-genotypes of many crabapple cultivars used for cross-pollination have not yet been reported. In this study, seven crabapple cultivars were genotyped, and the genomic DNA of one novel S-allele in ‘Mt. Blanc’ and three variants of previously discovered alleles in ‘Manchurian’, ‘Snowdrift’ and ‘Indian Summer’ were characterized. Genomic DNA sequences were submitted to National Center for Biotechnology Information (NCBI) GenBank, and PCR-based detection methods were developed. The methods and results of this study aim to enrich S-genotyping methodologies and inform pollinizer-cultivar compatibility in commercial orchards.