Across the world, the keeping of stingless bees is increasingly popular, providing commercial pollination, high-value honey and a rewarding pass time. The popularity of stingless beekeeping has resulted in large-scale anthropogenic movements of nests, sometimes from outside their native range. Colony movement has the potential to impact local populations via transfer of parasites and pathogens and gene flow across unnaturally large geographic scales. Tetragonula carbonaria is the most widespread and commonly kept stingless bee species in Australia. Concerns have been raised that large-scale artificial propagation of T. carbonaria colonies by Sydney beekeepers, from a small number of colonies that originated in south-east Queensland, may have two consequences. First, the managed population may be becoming increasingly inbred. Second, the wild population may be experiencing significant introgression of south-east Queensland genotypes, potentially diluting local adaptations to the Sydney environment and resulting in the loss of local alleles. Here we show, based on microsatellite and mitochondrial markers, that both the managed and wild Sydney populations are significantly different from the south-east Queensland population. Nonetheless there is evidence that introgression of south-east Queensland alleles is impacting the genetic structure of both wild and managed Sydney populations. The two Sydney populations are indistinguishable, suggesting two-way gene flow in Sydney consistent with expectations of gene flow via male dispersal. All populations have low inbreeding coefficients, suggesting that they are genetically healthy.