The apple maggot fly, Rhagoletis pomonella, is a major pest of apples in the eastern United States. Prior to the introduction of apples <300 years ago, R. pomonella infested native hawthorns (Crataegus sp.) and has only recently undergone a host shift to attack apples. The genetic variation needed to rapidly exploit the novel apple host was likely present in populations before the host shift. Recent evidence suggests introgression from populations in Mexico. Localizing the origin of this genetic variation is difficult, as the genetic structure of Mexican populations is unknown. Further, within Mexico, two different biogeographical zones may inhibit gene flow not only between Mexican populations, but between Mexican and U.S. populations as well. These biogeographic zones roughly correspond to the Trans-Mexican Volcanic Belt (TMVB) and the Sierra Madre Oriental Mountains (SMO). We analyzed population genetic structure in Mexico using microsatellites across 18 populations, including 3 sites in the U.S. Within both Mexican biogeographic zones, we detected isolation by distance. A significant difference in genetic diversity was found between zones, with SMO having twice the number of alleles and heterozygosity. Large and significant F_ST values differentiated Mexican populations across the two biogeographic zones (average pairwise F_ST=0.30). However, less genetic differentiation was found between U.S. and SMO populations (average pairwise F_ST=0.14) than between SMO and the TMVB. Low differentiation over large distances suggested a recent population expansion from northern SMO populations into the U.S. after the recession of Pleistocene glaciers (~20,000 years ago). This study indicates that genetic variation found in SMO was retained as populations expanded into the U.S., better enabling the host shift from native hawthorns to introduced cultivated apples, and facilitating the elevation of a native species to pest status.