Technical Abstract: Accurate inference of genetic discontinuities between populations is an essential component in studies of intraspecific biodiversity and evolution, as well as associative genetics. Multi-locus genotypes were amplified from 949 individuals representing seedling trees from 88 half-sib families from eight M. sieversii populations collected in Kazakhstan. Analyses using a hierarchical model to estimate Fst showed that differentiation among individual families is more than three times greater than differentiation among sites. In addition, average gene diversity and allelic richness varied significantly among sites. A rendering of a genetic network among all sites showed that differentiation is largely congruent with geographical location. In addition, non-hierarchical Bayesian assignment methods were used to infer genetic clusters across the collection area. We detected four genetic clusters in the data set. The spatial pattern of genetic assignments among the eight collection sites shows two broadly distributed and two narrowly distributed clusters. These data indicate that the southwestern collection sites are more admixed and more diverse than the northern sites. Estimates of structure and admixture can be exploited when developing representative core sets for allele mining.