The genetic origins of species may not all trace to the same time and place as the proximate cause(s) for population divergence. Moreover, inherent gene-flow barriers separating populations may not all have evolved under the same geographical circumstances. These considerations have lead to a greater appreciation of the plurality of speciation: that one geographical mode for divergence may not always be sufficient to describe a speciation event. The apple maggot fly, Rhagoletis pomonella, a model system for sympatric speciation via host-plant shifting, has been a surprising contributor to the concept of speciation mode plurality. Previous studies have suggested that past introgression of inversion polymorphism from a hawthorn-fly population in the trans-Mexican volcanic belt (EVTM) introduced diapause life-history variation into a more northern fly population that subsequently contributed to sympatric host race formation and speciation in the United States (US). Here, we report results from a microsatellite survey implying (i) that volcanic activity in the eastern EVTM may have been responsible for the initial geographical isolation of the Mexican and northern hawthorn-fly populations c. 1.57 mya; and (ii) that flies in the Sierra Madre Oriental Mountains (SMO) likely served as a conduit for past gene flow from the EVTM into the US. Indeed, the microsatellite data suggest that the current US population may represent a range expansion from the northern SMO. We discuss the implications of these findings for sympatric race formation in Rhagoletis and speciation theory.