A revision of the species of Hymenophyllum subg. Hymenophyllum in the Brazilian Atlantic forest domain is presented. Morphological and molecular analyses were performed, based on herbarium material and samples collected during fieldwork. For the molecular analyses, data of the plastidial markers rbcL, rbcL-accD, rps4-trnS and trnG-trnR were used. The analyses demonstrated the existence of three distinct and independent lineages of subgenus Hymenophyllum in Atlantic forest domain. Three taxa were recognized: H. fucoides, H. megachilum, and an additional new species, H. bradeanum, a narrow endemic to the Itatiaia Massif, southeastern Brazil. Distribution maps, identification keys, descriptions and illustrations are present, together with an update of the conservation status of the species.