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.