Several species of mosquito in the Anopheles gambiae species complex are highly efficient vectors of malaria in sub-Saharan Africa. Two of these species, An. coluzii and An. gambiae, have only recently been elevated to the level of separate species, and were previously thought to be separate forms of the same species. Genome scans have revealed a region of high divergence on the left arm of the third chromosome (3L), containing at least 6 genes of the thioester-containing protein (TEP) family, which have been implicated in the innate immune response. Interestingly, An. coluzzii populations from Mali and Burkina Faso are fixed for an allele at TEP1 – rB, not present in sympatric An. gambiae populations – that confers additional resistance to the malaria parasite. To annotate the TEP Anti-Pathogen Locus (TAPL) and identify structural variation among the three known haplotypes – rB, rA, and S – in the TAPL region, we have sequenced BAC clones and generated consensus sequences of each of the three haplotypes. Sequence alignments indicate several significant structural differences between the three haplotypes, including a duplication in one haplotype that has created a novel chimeric TEP gene. TEP1 had previously been shown to be the product of a similar chimerization, suggesting that this may be an under-appreciated mechanism of gene creation and genome evolution in Anopheles mosquitoes.