Abstract: Numerous studies of tephritid species have revealed important elements of population-level variation. Geographic patterns in genetic variation may indicate the presence of unrecognized species complexes or reveal the pattern of introduction of a species to new geographic regions. Many tephritids use multiple hosts, and studies of host-associated variation have led to insights on the evolution of new species and on the management of pests. In all cases, better information on the genetic structure of populations within a species lead to more effective management strategies. Anastrepha obliqua is a widespread pest in the Neotropics. In Mexico, ecological studies have documented an interesting pattern of seasonal use of multiple host plants. Given existing knowledge about the influence of host use on population biology and structure in Rhagoletis and other taxa, we have developed numerous nuclear and mitochondrial genetic markers to examine levels of population structure in this taxon. These data will be combined with ecological and behavioral studies to examine potential mechanisms for generating information about the breeding structure of A. obliqua populations. This study could serve as a model for the analysis of other related species of interest. We report the evidence for host-associated, temporal, and geographic population structure in A. obliqua.