Technical Abstract: Genetic diversity and disease resistance are described for 496 seedlings from wild populations of Malus orientalis collected in southern Russia and Turkey in 1998 and 1999. Eighty five half-sib families were genotyped using seven microsatellite markers and disease resistance was determined for apple scab (Venturia inaequalis Cooke), cedar apple rust (Gymnosporangium juniperi-virginianae Schwein) and fire blight (Erwinia amylovora Burrill). Of the M. orientalis seedlings assayed for disease resistance, 76 were resistant to scab and fire blight, 16 were resistant to scab and cedar apple rust, 11 were resistant to fire blight and cedar apple rust, and 20 were resistant to all three diseases. Seedlings genotyped from the four Turkish collection locations were more diverse than those genotyped from the two Russian Caucasus locations. Bayesian analyses of the population structure revealed six distinct clusters. Most of the individuals segregated into two clusters, one containing individuals primarily from southern Russia and the other containing individuals from both Russia and northern Turkey. Individuals in the four small clusters were specific to Turkish collection locations. These data suggest wild populations of M. orientalis from regions around the Black Sea are genetically distinguishable and show high levels of diversity.