We investigated S-RNase genotypes of nine useful Afghan apple cultivars including six original cultivars and one rootstock. We also determined S-RNase genotypes of 11 apple cultivars and lineages and seven rootstocks in Japan. We speculated regarding the unidentified parents of cultivars and lineages from the S-RNase genotypes and their fruit and branch characteristics and also identified mistaken parents. We compiled a database of the apple S-RNase genotypes of 622 apple cultivars investigated, which included a survey system of cultivar combinations showing those that were fully incompatible, semicompatible, and fully compatible, written in the Pashto language.