Loss of rainforest because of agricultural and urban development may impact the abundance and diversity of species that are rainforest natives. Tropical fruit flies are one group of such organisms indigenous to rainforests. In southeast Queensland, a region subject to rapid urbanization, we assessed the impact of habitat disturbance on the distribution and abundance of native fruit flies. Data on four species (Bactrocera tryoni, Bactrocera neohumeralis, Bactrocera chorista, and Dacus aequalis) were gathered and analyzed over 6 months in three habitat types: suburbia, open sclerophyll forest, and rainforest. We also analyzed the data at a combined "dacine fruit fly" level incorporating all fruit fly species trapped over the period of study (as might occur in a biodiversity assessment): these included the four species already named and Bactrocera melas, Bactrocera bryoniae, Bactrocera newmani, and Dacus absonifacies. Analysis at the species level showed that the polyphagous pest species responded differently to the monophagous species. Bactrocera tryoni, which has more exotic than native hosts, was positively affected by transformation of natural habitat into suburbia whereas B. neohumeralis, which has nearly identical numbers of native and exotic hosts, was found equally across habitat types. Bactrocera chorista and Dacus aequalis, each monophagous on a species-specific rainforest host plant, were most abundant in rainforest. The analysis based on the combined data suggests that replacing rainforest with suburbia has a neutral, or even positive, effect on the abundance of fruit flies as a whole. At the species level, however, it can be seen that this is an erroneous conclusion biased by the abundance of a single pest species. Our discussion raises the issue of analyses at supraspecific levels in biodiversity and impact assessment studies.