We have sequenced the AT-rich control region of the mitochondrial DNA (mtDNA) of six species in the Afrotropical Anopheles gambiae complex and the closely related A. christyi. Contrary to expectations, the AT-rich region in this group is evolving rather slowly, more slowly than the third position of mtDNA protein-coding 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 endemic A. bwambae as a sister taxon to A. 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 of A. arabiensis. The anomalous position of this species can be explained by introgression with A. gambiae. From the phylogenetic position, we could infer mtDNA gene flow from A. gambiae to A. arabiensis.