A Japanese endemic liverwort Calypogeia asakawana S.Hatt. ex H.Inoue has been considered peculiar within the genus Calypogeia (Calypogeiaceae) due to its unique morphological characters, while the phylogenetic relationships within the family have up to now not been evaluated. To assess its sound taxonomic placement, we newly acquired DNA data for C. asakawana and the phylogenetic analysis is conducted based on the sequences of chloroplast rbcL, rps4, trnT-L-F and trnG regions. The inferred tree supports the position of C. asakawana distinct from other Calypogeia accessions, warranting description of a new genus to accommodate the species. Here we newly describe Protocalypogeia for C. asakawana and provide a revised key to the genera of Calypogeiaceae.