Technical Abstract: The diversity of landrace and heirloom fruit varieties has declined worldwide over the past century. Abandoned farmsteads and historic orchards harbor considerable agrobiodiversity, but the extent and location of that diversity is poorly understood. We assessed the genetic diversity of 280 historic apple (Malus Xdomestica) trees growing in 43 abandoned farmstead and orchard sites in Arizona, Utah, and New Mexico using seven microsatellite markers. We compared the historic “unknowns” to 109 heirloom varieties introduced into the Southwest in the late 19th and early 20th centuries. Genetic analysis revealed that 144 varieties were represented in the 280 field samples. We identified 34 of these 144 varieties as named heirloom varieties brought to the region by Stark Brothers Nursery and by USDA as well as agricultural experiment stations. One hundred and twenty of the total samples (43%) had DNA fingerprints that suggested that they were representative of these 34 named varieties. The remaining 160 samples—representing 110 varieties—had unique fingerprints that did not match any of the named varieties. The results of this study confirm for the first time that a high diversity of historic apple varieties remain in homestead orchards on and near the Colorado Plateau. Future efforts targeting orchards in the Southwest should focus on conservation for all unique genotypes as a means to sustain both cultural heritage and biological genetic diversity.