The apple maggot, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), is a serious introduced quarantine pest in the apple (Malus spp.)-growing regions of central Washington and Oregon. In August 2011, seven fly larvae of unknown origin were discovered infesting fruit of an exotic Chinese crabapple, Malus spectabilis (Aiton) Borkhausen, in Kennewick, Benton County, WA. If confirmed, Chinese crabapple would have represented a new host for R. pomonella in Washington and triggered quarantine measures in a surrounding three-county region of the state. Here, we establish, based on five microsatellite loci, the identity of the crabapple-infesting larvae as the western cherry fruit fly, Rhagoletis indifferens Curran, representing a new host record for the fly. Morphological analysis of six flies reared to adulthood confirmed the genetic identification. The results demonstrate the utility of integrating rapid genetic identification methods with field surveys of economic pests, which decreased detection times by months, and avoided enacting costly quarantine measures that saved local and federal bodies >US$0.5 million in monitoring, inspection, and control costs. We discuss current ongoing efforts to develop rapid, accurate, and inexpensive on site DNA-based detection tools for R. pomonella that would have general applicability for the control of pest insects.