The red algal genus Stenogramma (Gigartinales, Phyllophoraceae) was not recorded in the Indian Ocean. In this study, we used molecular assisted alpha taxonomy to assess the algal diversity of the algal flora of the southern coasts of Madagascar. Using COI-5P sequences as barcode marker and LSU and rbcL sequences to infer phylogenetic relationships, a novel species of Stenogramma has been uncovered at Manantenina, Anosy, Madagascar, which is here described. The species diversity within the genus Stenogramma is discussed and in light of our phylogenetic inference we hypothesized that species of northern and southern hemispheres may have diversified separately. This novel species, being found on subtidal rocks surrounded by sands, the habitat preference of the genus is discussed.