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Halymenia malaysiana, one of the foliose species of Halymenia was first reported from Malaysia and showed some morphological features that distinguish it from sister species, such as Halymenia dilatata, Halymenia maculata, and Halymenia porphyraeformis. In this study, Halymenia samples were collected from nine locations along the coast of Viet Nam (8°–17°N) in the South China Sea and Gulf of Thailand. Morphological observations indicated that almost all samples were Halymenia malaysiana which was supported by two genetic markers, rbcL and COI-5P. However, the presence of Halymenia dilatata in Viet Nam is still unresolved. Based on rbcL, the common haplotype in Viet Nam was R1 as in Malaysia and three new haplotypes were added to H. malaysiana for Southeast Asia. Genetic differences were evident between the Sunda Shelf (Viet Nam and Malaysia) populations and those in Philippine waters. We suggest that a combination of morphology and molecular data would be useful to accurately assess the species diversity and phylogeography of Halymenia in Viet Nam and Southeast Asia region.