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Through the sequencing of the complete mitochondrial genome of three individuals of Malagasy ancestry, we completed the characterization of the island southeastern Asian specific M46 haplogroup. We assumed that the association of the np 3588 and np 16278 polymorphisms were M46 specific. In addition, we characterized a novel basal M subhaplogroup: M23. This clade can be defined by one coding region transition at np 10295 and one control region transition at np 16263. Our data suggest the arrival of South Asian migrants before the start of the 15th century and highlights the fact that future studies dealing with the settlement of Madagascar should consider at least three potential source populations (Africa, Indonesia, and India).