Since 1985, a new and serious fruit fly pest has been reported in northwestern Australia. It has been unclear whether this pest was the supposedly benign endemic species, Bactrocera aquilonis, or a recent introduction of the morphologically near-identical Queensland fruit fly, B. tryoni. B. tryoni is a major pest throughout eastern Australia but is isolated from the northwest region by an arid zone. In the present study, we sought to clarify the species status of these new pests using an extensive DNA microsatellite survey across the entire northwest region of Australia. Population differentiation tests and clustering analyses revealed a high degree of homogeneity within the northwest samples, suggesting that just one species is present in the region. That northwestern population showed minimal genetic differentiation from B. tryoni from Queensland (FST=0.015). Since 2000, new outbreaks of this pest fruit fly have occurred to the west of the region, and clustering analysis suggested recurrent migration from the northwest region rather than Queensland. Mitochondrial DNA sequencing also showed no evidence for the existence of a distinct species in the northwest region. We conclude that the new pest fruit fly in the northwest is the endemic population of B. aquilonis but that there is no genetic evidence supporting the separation of B. aquilonis and B. tryoni as distinct species.