Hymenophyllum subg. Mecodium is subcosmopolitan and comprises ca. 35 species. Its neotropical species are poorly known taxonomically. The high degree of morphological similarity among the species and the absence of clear characters to distinguish them has confounded taxonomic treatments, resulting in the lumping of many putative segregate taxa into a broadly circumscribed Hymenophyllum polyanthos species complex. The goal of the present study was to analyze morphologically and phylogenetically the species of Hymenophyllum subg. Mecodium in the Atlantic Forest domain. Morphological studies were conducted utilizing traditional stereomicroscopy and scanning electron microscopy (SEM). Additionally, Bayesian inference and maximum likelihood phylogenetic analyses were performed using plastid data for seven markers: atpB, atpB-rbcL, matK, rbcL, rbcL-accD, rps4, and rps4-trnS. Seven independent lineages were identified in this study, while morphological analysis supported the delimitation of five taxa within the Atlantic Forest domain: Hymenophyllum apiculatum, H. polyanthos, H. schomburkii, H. undulatum, and H. viridissimum. One taxon, Hymenophyllum sturmii, is recognized as a cryptic species, formed by two independent evolutionary lineages, and treated here provisionally as the H. sturmii complex. A taxonomic revision for the six taxa occurring in the Atlantic Forest domain is presented, including seven new lectotypifications, along with an identification key, descriptions, and illustrations for the species. We also provide data regarding the geographical distribution and conservation status of these six species.