Genetic integrity is still maintained in natural populations of the indigenous wild apple species (Mill.) in Saxony as demonstrated with nuclear SSR and chloroplast DNA markers.

(Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry, and urbanization increasingly endanger natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple (Borkh.) threaten the genetic integrity of . The present study investigated the number of hybrids, genetic diversity, and genetic structure of 292 putative that originate from five different natural populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony. Eighty-seven percent of the wild apple accessions were identified as pure . The cpDNA analysis showed six private haplotypes for whereas three haplotypes were present in and . The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure and individuals indicating a low gene flow between both species. The genetic diversity within the pure populations was high with a weak genetic structure between the populations indicating an unrestricted genetic exchange between these populations. The clear distinguishing of and confirms our expectation of the existence of pure accessions in this area and supports the argument for the implementation of preservation measures to protect the populations in Saxony.