Cyanopyrenia japonica Harada, gen. et sp. nov. is described. It is characterized by having a coccoid cyanobiont, perithecia, sparsely branched paraphyses, thin-walled bitunicate asci, and simple hyaline spores. It resembles Verrucaria, Pyrenocollema, and some Lichinaceae in certain morphological respects, but has no clear affinities. It is known only from the type locality in Shikoku, southwestern Japan, where it grows on frequently submerged rocks in the main flow of a river.