Technical Abstract: Plant explorers have gathered seeds from wild Malus sieversii trees in Kazakhstan which are believed to be one of the major progenitor species of the dessert apple, Malus x domestica. Large field and seed collections from these explorations are maintained at the Plant Genetic Resources Unit in Geneva, NY as part of the USDA National Plant Germplasm System (NPGS). Seven highly polymorphic microsatellite markers were selected to assess the genetic relationships among the trees in the field collections that represent the populations and the collection sites. Resulting population graph networks demonstrate that there is a significant among-site differentiation and that the collection is highly diverse. In addition, we developed core collections that considered molecular and quantitative traits to maximize the diversity of the entire collection within the smallest possible subset. These core collections serve as representative panels of the 949 individuals in the NPGS M. sieversii field collection. Breeders and researchers are using these more manageable core collections to screen for desirable new alleles for disease or environmental stress resistance.