During the Atimo Vatae research cruise of 2010, the seaweed flora of the southern coast of Madagascar was extensively sampled. Here we report on the species diversity and biogeographic affinities of the brown algal order Dictyotales, which was assessed using DNA-barcoding makers. Molecular identification resulted in 23 MOTU's belonging to 9 genera. From a biogeographic perspective Madagascar is considered to be part of the large tropical Western Indo-Pacific realm. However, only 3 out of 23 species confirmed this affinity. In contrast, species- and genus-level links to the more temperate coast of KwaZulu-Natal were as prominent (4 species) and 6 species represent endemic species. The remaining species were either widely distributed in tropical regions or their affinities were unclear. In conclusion, the Dictyotales data do not suggest the flora of southern Madagascar is unequivocally a part of the tropical Western Indo-Pacific realm, but rather a region of overlap, where more temperate species thrive in conjunction with some Indo West Pacific (IWP) elements.

The marine macroalgae of Madagascar have been poorly studied, probably due to difficulties in accessing most of the 4,828 kms of coastline spreading across more than 14° of latitude. Recent collecting trips in the southern and northern sections of the island provided large collections to contribute towards a better knowledge of the marine macrophyte diversity of Madagascar. The present study focuses on the brown macroalgal genus Sargassum. Based on morphological and molecular analyses of the nuclear ITS2, chloroplastic partial RuBisCO operon and mitochondrial cox3 and 23S, we delineated a total of 11 taxa including seven new records (*) for Madagascar and an unidentified taxon: S. elegans*, S. ilicifolium, S. ilicifolium var. acaraeocarpum*, S. incisifolium, S. cf. latifolium, S. obovatum*, S. polycystum, S. portierianum*, S. robillardii*, S. swartzii* and S. sp In addition, nine taxa listed in the literature were not found during these recent collecting trips, implying a possible full list of 20 Sargassum species for Madagascar. More collections are required for a comprehensive revision of the Sargassum diversity of the island, particularly along its west and east coasts.

We present a molecular survey of the species in the green algal genus Codium that were collected as part of the Atimo Vatae expedition to southern Madagascar. Based on clustering analysis of partial tufA and rbcL sequences, we recognize 11–12 species-level clusters in this area. Through a combination of morphological identifications and DNA comparisons, these clusters are identified as C. mozambiquense, C. spongiosum, C. lucasii subsp. capense, C. duthieae, C. decorticatum, C. prostratum, C. dwarkense, C. taylorii, C. arenicola and C. cf. cicatrix, and a new ball-shaped species. We present a phylogenetic tree inferred from a concatenated alignment with tufA, rbcL and rps3-rpl16 to show the placement of these species in the broader context of the genus and to analyse the biogeographic affinities of the southern Madagascan Codium flora. We conclude that the Madagascan flora shares elements with temperate South Africa and contains tropical Indo-Pacific elements. It also has endemic elements, some clearly at the species level, some possibly representing isolated populations of more widely-ranging species.

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.

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.

We evaluated the relationships among species in the genus Gelidiella using 47 rbcL and 29 COI sequences, including those from 18 specimens collected in Madagascar. Molecular analyisis revealed the presence of three major lineages among Magalasy Gelidiella which were assigned, based on morpho-anatomical observation, to Gelidiella acerosa, G. ligulata and a so far not described species for which we here proposed the name G. incrassata. Both molecular and morphological data demonstrated the presence of three species in Madagascar: the G. acerosa complex, G. ligulata, and G. incrassata sp. nov., described here. Gelidiella incrassata was collected on small gravel from the intertidal down to a depth of 14 m on the southeast coast of Madagascar. It is distinguished by its large size (up to 7 cm), opposite to alternate ramuli, thick-walled cortical and medullary cells, and stalked tetrasporangial stichidia with irregular arrangement of tetrasporangia. Phylogenetic analyses of rbcL and COI sequences revealed the sister relationship between G. incrassata and G. fanii from southeast Asia and Hawaii. Gelidiella acerosa comprised three genetic groups in Madagascar, each being genetically distinct (pairwise distances, 4.9–8.3% for COI and 1.2–2.3% for rbcL). Further sampling of G. acerosa is needed before taxonomic revisions can be proposed. The distribution of G. ligulata is expanded to include the southwest Indian Ocean.