Technical Abstract: Plant domestication is generally modeled as a scenario wherein strong artificial selection is applied to a small subset of the population of a wild species. The result is that the domesticated species exhibits a genome-wide reduction in genetic variation, referred to as a genetic bottleneck. This pattern has been observed for many cultivated plants, and is especially prominent for annual, selfing crops such as rice and soybean. In contrast, genetic bottlenecks in clonal, outcrossing, and/or perennial crops can be less severe than those seen in annual selfers. This is especially true if the crop is brought in to cultivation multiple times, or if the crop’s gene pool has been supplemented by gene flow from wild relatives. Here, we examine the genetic diversity present in populations of both ancient (cider apple) and modern (dessert apple) Malus x domestica cultivars, as compared to their wild relatives M. sieversii, M. sylvestris, and M. orientalis, using between six and 19 SSR loci. The severity of the genetic bottleneck associated with the domestication of M. x domestica will be compared to those found in other domesticated plants with a variety of life histories and mating systems.