Anastrepha ludens and A. obliqua are considered pests species of economic concern whose geographic range stretches from the southern tier states of the United States to Central America (A. ludens) and South America (A. obliqua). This research aims to investigate the phylogeographic structure of these two species utilizing sequence-based methods. Here, we convey the results from the exploration of COI and ND6 mitochondrial regions in individuals from sixty-six A. ludens and seventy-two A. obliqua geographic collections. We report the patterns of geographic variation, levels of population structure, gene flow, and dispersal patterns for these two economically important agricultural pests. Additionally, we highlight the importance of these descriptive genetic data in developing pest mitigation strategies as they provide valuable insight into the local and regional migration patterns.