Malus sylvestris is the only apple species native to Central Europe. Its genetic integrity may be threatened by hybridization with the cultivated apple (Malus × domestica). A total of 883 genotypes, 477 putative wild apples in Germany and Luxembourg and 406 old to modern cultivars has been investigated. Wild apples growing in Germany originated from Rhineland-Palatinate, North Rhine-Westphalia, Saxony-Anhalt and Saxony. The genetic structure was analysed at ten isozyme marker loci, and morphology was studied by fruit size, leaf pubescence, and a complex morphological description performed in advance. A model-based cluster analysis applied to all nuclear data resulted in two clearly differentiated gene pools for putative wild and cultivated apples with moderate proportions of admixture in the wild group on average (0.138 total, 0.111 German sample). At the individual level, the percentages of both hybrids and feral cultivars together ranged from 2.3% in Rhineland-Palatinate to 28.8% in Luxembourg. The intraspecific variability in fruit diameter ranged from 21 to 40 mm, and that in leaf pubescence in autumn ranged from score 0 to score 1. No single morphological trait of a specimen appeared to be sufficient for identification. Even the correspondence between the complex morphological and complex genetic determinations for individuals did not exceed 93% in pure wilds and 64% in hybrids. Genetic variation in pure wild apple is high (species level: P = 90%, A/L = 3.1, He = 0.369). Allelic differentiation & was 0.089, pairwise genetic distance (d0) ranged from 0.065 to 0.148 among five samples. Correspondence between genetic and geographic distance of populations was observed to a certain extent.

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