Technical Abstract: Malus sieversii is one of the major progenitor species of the dessert apple, Malus x domestica. Wild M. sieversii trees are found in the mountainous regions of Kazakhstan and other central Asian countries. The Plant Genetic Resources Unit (PGRU) in Geneva, NY maintains large field and seed collections of these materials as part of the USDA National Plant Germplasm System. We conducted a hierarchical analysis of genetic structure of this collection using seven highly diverse microsatellite markers. We displayed the genetic relationships among populations and the collection sites using population graph networks. These data show that the collection is highly diverse and that there exists a significant amongsite differentiation. In addition, we developed core collections that maximize the diversity of the entire collection within the smallest possible subset using both genotypic and phenotypic trait data. These core collections serve as representative panels of the 949 individuals in the PGRU M. sieversii field collection. Breeders and researchers can make use of these more manageable core collections as they screen for desirable new alleles for disease or environmental stress resistance.