A species complex is a group of closely related species whose ecological or morphological boundaries are sufficiently vague that delimiting one species from another is difficult. In Australia, a group of four stingless bee species – Tetragonula carbonaria Smith, Tetragonula hockingsi Cockerell, Tetragonula mellipes Friese, and Tetragonula davenporti Franck – form a species complex in which gross morphology is clinal and overlapping. The species are most readily distinguished by the morphology of their brood combs. Here we genetically characterize bees sampled in areas where the species do and do not have contact. Our data corroborate previous evidence that T. hockingsi and T. carbonaria are genetically distinct and that there are two genetically distinct groups of T. hockingsi – one in the north and the other in the south of Queensland. Curiously, northern populations of T. hockingsi, which are allopatric to T. carbonaria, are genetically closer to T. carbonaria than are southern populations of T. hockingsi, which are in sympatry with T. carbonaria. We detected three hybrid colonies that appear to have arisen because of anthropogenic movement of T. hockingsi colonies from north to south of Queensland where males mated with local T. carbonaria queens. We discuss the status of T. davenporti, a recently described species cryptically similar to T. hockingsi from south-east Queensland.