© 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Deutschland, ein Teil von Springer Nature.Kyrgyzstan is among the mother lands of apple and thus quite rich in apple genetic resources. This study was conducted to determine S‑allele profiles of apple genotypes collected from different regions of Kyrgyzstan. The apple materials used belonged to 4 different species (M. domestica, M. kirghisorum, M. sieversii, M. niedzwetzkyana) and a total of 137 genotypes were evaluated in the study. Scorable bands were obtained with the use of 11 primer combinations and band lengths varied between 210 ± 50 and 700 ± 50 bp. Present findings revealed the most common S‑allele as S46. Present findings are expected to provide contribution in selection of pollinator and main cultivar while establishing new orchards.