An inventory of Phlebotomine sandflies was carried out in the Ankarana tsingy located in far northern Madagascar. A total of 723 sandflies were used for morphological, morphometric, and molecular studies (sequencing of partial cytochrome B (mtDNA) and partial 28S (rDNA)). Nine species were identified: Phlebotomus fertei, Sergentomyia anka, Se. sclerosiphon, Se. goodmani, two species of the genus Grassomyia, as well as three new species described herein: Se. volfi n. sp., Se. kaltenbachi n. sp., and Se. ozbeli n. sp. The recognition of these new species is strongly supported by molecular analyses. The first two of the new species could not be classified into any existing subgenus, therefore we proposed two new subgenera (Ranavalonomyia subg. nov., and Riouxomyia subg. nov.), with combinations as: Sergentomyia (Ranavalonomyia) volfi and Sergentomyia (Riouxomyia) kaltenbachi. Our study reveals important molecular variability in Se. anka, with the recognition of a population whose taxonomic status remains below that of species. Our research confirms the need to further study the specific diversity of Malagasy sandflies, which until the start of this millennium remained mostly unknown.