Technical Abstract: The USDA-ARS National Plant Germplasm System (NPGS)-Plant Genetic Resources Unit (PGRU) apple collection in Geneva, NY conserves over 2500 trees as grafted clones. We have compared the genotypes of 1131 Malus x domestica cultivars to a total of 1910 diploid materials representing 41 taxonomic designations in the NPGS collection to identify those that are genetically identical based on nine microsatellite markers. We calculated the probability of identity of these individuals based on allelic diversity and, when possible, used fruit images to qualitatively confirm similarities. A total of 237 alleles were amplified from nine SSR loci. The variation in marks was adequate to assess duplication within the collection, with the caveat that “sport families” would likely not be differentiated. A total of 238 M. × domestica and 10 samples of other taxonomic groups shared a genotype with at least one other individual. In several cases, genotypes for cultivars matched genotypes of known rootstocks, and it appears as if these specific accessions may not accurately represent the indicated named clones. Sets of individuals with identical genotypes and similar cultivar names were assigned to sport families. These 23 sport families, represented by a total of 104 individuals, may have mutations that could not be identified using the 9 SSR markers. Five of the selected markers (CH01h01, CH02d08, CH01f02, G12, GD147) overlap with sets of markers that have been used to fingerprint European apple collections, thus making future efforts to coordinate collection inventories possible.