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Little is known about the genetic diversity and phylogeographic structure of seaweeds in Southeast Asia particularly for Halymenia species. Herein, molecular analyses based on DNA sequences of the COI-5P and rbcL were performed to assess the genetic structure within the foliose Halymenia species H. malaysiana in Malaysia and the Philippines. A total of ten COI-5P haplotypes and eight rbcL haplotypes were recognized from 42 specimens of H. malaysiana examined in this study. The genetic diversities of H. malaysiana were relatively higher based on the COI-5P sequences compared with the rbcL sequences. The results showed that populations from Peninsular Malaysia (East, South, and West coast) were genetically homogenous and exhibited low level of genetic divergence from populations from East Malaysia. In contrast, populations from the Philippines were distinct from Malaysian populations …