Mitonuclear discordance has been widely reported in animal species. In stingless bees, the occurrence of mitonuclear discordance is favoured by the adopted colony-founding strategy [dependent colony foundation (DCF)], with phylopatric females and dispersing males. To address the extent to which the DCF system is reflected in the population structure of Partamona helleri, a stingless bee found in Brazilian Atlantic Forest, we sampled for sequences of maternally heritable mitochondrial DNA (mtDNA) and biparentally inherited nuclear microsatellite markers in workers from 339 colonies, covering its entire distribution range. We found evidence of mitonuclear discordance in P. helleri, which is compatible with the DCF strategy. Genetic structuring of the mtDNA was associated with the occupation of an area by few female lineages, and genetic structuring of the nuclear DNA was associated with isolation by distance. Phylogeographical analysis showed that the origin of P. helleri seems to have been in the region of the state of Bahia 860 000 years ago and that the divergence between the lineages began 520 000 years ago. From this primary centre of dispersal, a main north-to-south migration route occurred, resulting in the occupation of areas in the southern portion of the Atlantic Forest, probably favoured by the dynamics of evergreen forest expansions during the Quaternary.