Yonagunia, a genus of the red algal order Halymeniales, has never been recorded in the Western Indian Ocean. In this study, we used molecular assisted alpha taxonomy to assess the diversity of the marine algal flora of southern Madagascar. A combination of COI-5P and rbcL sequences, used as a DNA-barcode and phylogenetic marker respectively, revealed two species of Yonagunia from the Toliara region in the South of Madagascar. One species, is described a species new to science, Yonagunia atimo-vatae sp. nov. Sequences of the other species, matched of Polyopes ligulata, but it was resolved within the genus Yonagunia rather than Polyopes. Hence, a new combination Yonagunia ligulata comb. nov. is established.