We sampled a pest fruit fly species, the Queensland fruit fly, Bactrocera tryoni, across its entire ecological range in eastern Australia, from ancestral high-density populations in tropical regions through to isolated outbreak populations in marginal arid areas. Using DNA microsatellite markers, we found that in ancestral areas, population differentiation was low and populations were genetically homogeneous over large distances. In more temperate areas, populations were far more genetically differentiated but there was no pattern of isolation-by-distance (no drift/migration equilibrium). Genetic drift appeared to be the major influence on population differentiation. The transition between these extremes was abrupt and unexpectedly far from the species border. Limited geographic structuring among the non-equilibrium populations was apparent from patterns of genetic differentiation, patterns of allelic richness and an ordination analysis. Our results also suggested that there might be recurring migration of flies into a neighbouring quarantine area.