We investigated species in the family Phyllophoraceae from Korea using nuclear large-subunit ribosomal RNA, mitochondrial COI and plastid rbcL sequences and morphological examination. To understand the taxonomic relationships of Korean Ahnfeltiopsis, we also analysed topotype materials of A. leptophylla and Besa papillaeformis from California. Both individual and combined datasets revealed that Korean Ahnfeltiopsis (except A. flabelliformis) consistently formed a clade with Californian A. leptophylla and Besa papillaeformis with strong support, and this Besa clade was distinct from other genera or genetic groups in the Phyllophoraceae. The form and development of reproductive structures in topotype material of B. papillaeformis as well as those of the four Ahnfeltiopsis species supported the molecular phylogeny and underlined the distinctiveness of the Besa clade. We therefore propose to transfer four Ahnfeltiopsis species to the genus Besa as Besa catenata, B. divaricata, B. leptophylla and B. paradoxa. The concept of the genus Besa is extended to species having a heteromorphic life history and conspicuous erect gametophytes. On the basis of our molecular phylogeny, we restore A. flabelliformis to the genus Gymnogongrus. We describe a new member of the Phyllophoraceae, Schottera koreana sp. nov., a deep-water species occurring along western and southern coastlines of Korea.