During an inventory of Phlebotomine sand flies carried out in Madagascar, we have identified some specimens showing morphological characters related to the subgenus Sintonius of the genus Sergentomyia. We started a molecular study based on cytochrome b mtDNA and on D1–D2 and D8 domains of the rDNA. The sampling includes all the Sergentomyia species available and also S. ( Sergentomyia) schwetzi, S. ( Parrotomyia) magna, and the following species belonging to the subgenus Sintonius: S. clydei, S. christophersi, S. affinis vorax, S. adleri and S. meilloni. The Sintonius subgenus (sensu Theodor) is paraphyletic. The Malagasy specimens morphologically Sintonius-like are never clustered with the continental Sintonius. We propose a new subgenus to include them: Trouilletomyia subg. nov. Due to the lack of mesanepisternal setae, the species huberti is removed from the genus Phlebotomus and we propose here a new combination: Sergentomyia huberti comb. nov. The male of S. huberti is pinpointed and described for the first time. Lastly, a new species for Science is described on one female: Sergentomyia ( Trouilletomyia) boironis n. sp.
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