Technical Abstract: Malus sieversii, a wild relative of domestic apple, represents an important source of genetic variation for several horticulturally important traits including fruit quality and disease resistance. Collections made by the USDA in Kazakhstan have now been analyzed to determine the extent of diversity and genetic structure. The diversity and differentiation of more than 1000 M. sieversii individuals collected from 10 sites have been determined based on data collected from seven unlinked microsatellite loci and 21 quantitative traits. Bayesian assignment analyses identified 10 genetic clusters that are variously admixed among sites. These data can be displayed as a minimum spanning network that enables us to correlate genetic diversity with geographic distances. We have also identified core subsets of individuals that can be used in QTL mapping, allele mining, and other comparative genomic studies.