Regions of southern Florida and southern Texas (extending into Mexico) provide the overwintering source populations for virtually all fall armyworm infestations affecting the continental United States. Understanding how these migratory populations annually disperse is important to predict and control infestations by this specific pest and to more generally investigate the environmental factors that influence the long-distance movements of flying insects. The two overwintering locations are associated with differences in the distribution of certain mitochondrial haplotypes that overlap in the region near the border separating the states of Alabama and Georgia. This provided an opportunity to test the resolution of the haplotype method by comparisons between smaller geographical areas and shorter time frames than previously examined. Correspondences were found between trap-capture numbers, fall armyworm strain proportions, and haplotype ratios calculated for individual counties and within season time periods that were generally consistent with expectations, providing confidence that those population movements could be accurately inferred. The comparison of haplotype distributions identified a migratory boundary separating the Texas and Florida populations coincident with the eastern edge of the Apalaehicola—Chattahoochee—Flint River basin. Calculations of strain numbers based on genetic markers revealed similarities and differences in strain population dynamics that can be applied to study the migratory behavior of fall armyworm subpopulations. The use of this methodology for the detailed mapping of migratory pathways and the identification of factors that influence the direction and extent of pest migration are discussed.