Pollination is essential for producing temperate-zone tree fruits like apples ( × ). While traditionally considered insect-dependent, this view may result from orchard designs tailored to European honeybees. Previous research showed that low-seed apples could develop in insect exclusion nets, suggesting wind as an alternative pollinator. This study investigated the paternal origin of seeds and fruit set under nets compared to open canopies. Netted canopies of 'Gala', Fuji', and 'Honeycrisp' set commercial fruit numbers without manual thinning. To determine the parental source of seeds, genotyping was performed using 16 SNP markers tailored for distinguishing apple cultivars, with primer design and genotyping conducted via the KASP™ system. Results showed significant genetic overlap between seeds from netted and non-netted fruits and nearby pollinizers, ruling out self-pollination. Netted canopies retained fruits with similar or fewer seeds compared to abscised fruits in open canopies, indicating fruit set depends on the population's seed content rather than individual fruit seed count. These findings supporting the hypothesis that apple trees are adapted to utilize both wind and insect pollination. While wind pollination offers a sustainable approach, it requires adjustments in orchard design to ensure sufficient pollen transfer for reliable fertilization and yield.