:The Thai–Malay Peninsula separates the Andaman Sea from the Gulf of Thailand. This barrier is known to affect species distribution and genetic diversity of marine organisms. Biodiversity studies need a correct species taxonomy to interpret their biogeography; this is especially relevant in marine algae where morphological characters are few or cryptic. We address species distributions of the important macroalgal genus Halimeda. The combination of morphological data and chloroplast tufA gene sequences were used to identify species, and to reveal the variation among Halimeda species around the Thai–Malay Peninsula. The morpho-anatomical and molecular analysis showed eight species of Halimeda in Thai and Malaysian waters: Halimeda borneensis, H. discoidea, H. gigas, H. macroloba, H. micronesica, H. minima, H. opuntia, H. renschii, and two undescribed species. Three species, H. minima, H. renschii and H. micronesica, were reported for the first time from the area. Species variation was much greater in the Andaman Sea than in the Gulf of Thailand. Our results show great variation in species composition and genetic variation between the two sides of the peninsula, which could be due to differences in sea-surface currents and environmental differences between the two sides of this important marine barrier.