We investigated mitochondrial diversity and phylogeographic structure across all subspecies of the barn swallow (Hirundo rustica) to clarify evolutionary relationships, identify novel haplogroups, and assess the extent of hybridisation and maternal introgression. We analysed 580 complete H. rustica mitochondrial genomes together with twelve additional Hirundo species, three of which were newly obtained. We identified 553 unique haplotypes, including 166 previously undescribed ones, revealing high nucleotide diversity among subspecies. Phylogenetic analyses found five major haplogroups. Of these, a novel haplogroup (E) was discovered and ascribed to H.r. tytleri, previously considered part of H.r. erythrogaster. Comparative analyses with other Hirundo species support a southern African origin of H. rustica at the end of the Pliocene, followed by diversification and northward expansion. Our comprehensive dataset substantially refines the phylogeographic resolution of the species. We identify a novel haplogroup, clarify subspecies-level relationships, and reveal pervasive hybridisation and maternal introgression. These findings revise the evolutionary history of H. rustica and underscore the complexity of its population structure and gene flow. Beyond reconstructing lineage history, our study provides an evolutionary framework crucial for predicting environmental change responses and guiding migratory species conservation strategies.