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.