AbstractWe have sequenced the AT‐rich control region of the mitochondrial DNA (mtDNA) of six species in the AfrotropicalAnopheles gambiaecomplex and the closely relatedA. christyi. Contrary to expectations, the AT‐rich region in this group is evolving rather slowly, more slowly than the third position of mtDNA proteincoding genes. Despite being relatively conserved between species, we detected intraspecific and intra‐individual (heteroplasmy) variation in this region. Phylogenetically, we found we could place the rare endemicA. bwambaeas a sister taxon toA. melas, the same evolutionary position as indicated by chromosomal inversions. The outgroup,A. christyi, gave evidence of the root of the tree. In comparing the molecular trees with that deduced by chromosomal inversions, they are completely congruent with the exception of the placement ofA. arabiensis. The anomalous position of this species can be explained by introgression withA. gambiae. From the phylo‐genetic position, we could infer mtDNA gene flow fromA. gambiaetoA. ara