The Japanese Marchantia taxa belonging to sect. Papillatae of subg. Chlamidium have been taxonomically ambiguous for a long time because many species and infraspecific taxa have been described based on their broad morphological variation. In order to resolve this taxonomic problem, nearly 200 specimens including type material of names placed in the section were morphologically examined. Among them, 45 specimens collected during our recent field work in Japan were newly sequenced for phylogenetic analysis. The molecular analysis showed that Japanese plants belonging to sect. Papillatae should be partitioned into two distinct clades. The plants belonging to the two clades were distinguishable by the presence or absence of a dark median band on the thallus and the morphology of the appendage of ventral scales and gametangiophores. Geographic distribution and ecological habitats in Japan also support the partitioning into two distinct clades. We propose the new combination M. emarginata subsp. cuneiloba (≡ M. cuneiloba). We also suggest that M. emarginata subsp. cuneiloba and M. papillata subsp. grossibarba are the appropriate names for the plants belonging to each clade. The species previously described from Japan (e.g., M. radiata Horik., M. tosana Steph. and M. tosayamensis Steph.) were synonymized for both of them.