AbstractAim of study: The Caucasian apple (Malus orientalis Uglitzk.) is distributed throughout the Hyrcanian forest. The species keeps a gametophytic self-incompatibility reproduction system based on a single S-allele. In order to ensure a high mating probability and thereby long-term survival of the populations, a high S-allele diversity is needed.Area of study: Three populations of Caucasian apple along an altitudinal gradient in northern Iran were studied.Material and methods: Here, we evaluated the S allele frequency and genetic diversity based on a small set of individuals.Main results: Moderate genetic diversity within population and high genetic differentiation among populations are suggested. In total, 18 S-alleles were identified among the three populations with between 10 and 12 S-alleles at each population site.Research highlight: The diversity of S-alleles showed a significant positive correlation with altitude, which is consistent with the positive correlation of genetic diversity.