The release of genetically engineered apple trees raises the question of their potential environmental impact, and the transfer via pollen of transgenes to cross-compatible cultivars of Malus domestica and Malus species is deemed to be the greatest source for environmental exposure. The hybrid TNR 31-35, a descendant of Malus sieversii var. sieversii f. niedzwetzkyana, carrying a homozygous, dominant gene responsible for red pigmentation in all plant parts, was used to assess gene flow in an apple scion repository of genetic resources. The red pigmentation provides a morphological marker that enables large-scale evaluation of cross-fertilization under natural conditions. In two consecutive years, 60 and then 56 apple trees of 38 different Malus domestica cultivars were selected to serve as pollen-receptor trees. In these two years, 6876 and then 5513 seeds, respectively, were gathered from pollen-receptor trees located at different distances, 2–100 m from 15 pollen-dispenser trees. In total, 11 797 seedlings were examined. An average of 1.8% and 1.4%, respectively, of all seedlings obtained showed red-colored leaves. Considering both years of sampling, 69% of the seeds fertilized by TNR 31-35 were found at less than 10 m from the nearest pollen-dispenser tree. Almost 91% of all seeds fertilized by TNR 31-35 were found at less than 60 m from the nearest pollen-dispenser tree, which is equal to 30 adjacent trees along the row. In this study, pollen was dispersed at least 104 m. After phenotypical evaluation, seedlings selected as red-colored were investigated by simple sequence repeat (SSR) analysis. Each seedling was tested with at least one heteromorphic SSR-marker, which allows the verification of TNR 31-35 as the male parent. All but four seedlings showed one allele specific for the appropriate fruiting tree and the second allele specific for the pollen-dispenser TNR 31-35.