Most taxa of the genus Marchantia L. (Marchantiaceae) produce multicellular gemmae within gemma cups. They are discoid bodies with two notches and a trace of stalk. Although gemmae of Marchantia have been of interest to physiological and developmental studies, they have been rarely used as a taxonomic character. To improve understanding of the taxonomic significance of gemma morphology, we investigated gemmae of six Japanese Marchantia (including four subspecies) and provide comparative morphological descriptions and a key. Several characters of the gemmae, including size, shape, morphology of marginal cells, and the presence or absence of mucilage hairs were useful in species identification. Morphological similarity of gemmae between M. polymoprpha and M. paleacea, as well as between M. emarginata and M. pinnata, was consistent with the results of molecular phylogenetic analyses. We recommend that morphology of gemmae should be used as a new taxonomic character in the genus Marchantia.