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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.