We name and describe two new species, Isoetes jejuensis and I. hallasanensis, from Jeju Island, South Korea. These taxa are compared with related species in East Asia, including I. coreana and I. sinensis. The rugulate megaspore ornamentation of I. jejuensis differs from those other lsoetes species. Furthermore, I. hallasanensis varies from I. asiatica in its microspore ornamentation and chromosome number, although both species have an echinate megaspore ornamentation. These new species are tetraploid (2n = 44), whereas I. coreana is hexaploid (2n = 66).