Previous taxonomic studies reported that nine species of Martensia (i.e., Martensia albida, Martensia australis, Martensia bibarii, Martensia elegans, Martensia flammifolia, Martensia fragilis, Martensia jejuensis, Martensia projecta , and Martensia palmata ) occur on the Korean coast. Our recent Martensia collections from various localities in Korea contain many specimens with a huge range of morphological variation and are difficult to classify into the named species. In this study, we analyzed DNA sequences of rbc L and COI genes to access their phylogenetic relationships and to verify taxonomic status based on morphological observations. The molecular analyses revealed that only two species of Martensia occur in Korea ( M. albida and M. jejuensis ). Martensia albida is characterized by having entire margins of blades with a single band of networks, whereas M. jejuensis is distinguished from the other species by possessing projections along the margins of the networks and blades. Both molecular analyses and morphological observations revealed that M. flammifolia is a member of the genus Nitophyllum . Some features (e.g., thallus habit, branching patterns, blade morphology, positions of reproductive structures) are not reliable for species identification. Our results indicate that the rbc L and the COI gene have sufficient resolution for delimitation at both species and generic levels in the subfamily Nitophylloideae.