Sphaerocionium is the largest subgenus of Hymenophyllum and occurs mainly in tropical forests of the Neotropical Region. Species of Hymenophyllum occurring in Brazil are poorly known due to difficulties in species delimitation and the absence of detailed studies. The aim of the present study was to present a synopsis of Hymenophyllum subg. Sphaerocionium in the Atlantic Forest domain, based on molecular and morphological data. Field and herbarium specimens were morphologically analyzed by stereomicroscopy, optical microscopy, and scanning electron microscopy. Phylogenetic relationships were evaluated by sequence comparison of the plastidial regions trnG-R and rps4-trnS. Morphological and phylogenetic evidence led to the recognition of 14 taxa throughout the Atlantic Forest, five of which are endemic. The taxonomy and nomenclature of Hymenophyllum in Brazil are revised and 19 new lectotypifications are proposed. The conservation status and geographical distributions of all species are updated and a dichotomous key is provided.