The taxonomic subdivision of Cyatheaceae, a family containing over 600 species of scaly tree ferns, has troubled pteridologists for more than one century. Recent molecular analyses have revealed four monophyletic groups (Alsophila R. Br., Cyathea Sm., Gymnosphaera Blume, and Sphaeropteris Bernh.) within this family. However, one of the four groups, Gymnosphaera, was still submerged in Alsophila in a modern classification proposed by the Pteridophyte Phylogeny Group due to Gymnosphaera being phylogenetically underrepresented in previous studies. In this study, we add the sampling of Gymnosphaera from its main distribution area (southeastern Asia) and conduct phylogenetic analyses of datasets containing individual and combined five chloroplast DNA regions (rbcL, rbcL-accD, rbcL-atpB, trnG-trnR, and trnL-trnF) of 120 scaly tree ferns using three methods (maximum parsimony, maximum likelihood, and Bayesian inference). The result is congruent with previous studies, consistently resolving scaly tree ferns as four well-supported clades with Sphaeropteris sister to the other three, and shows a probability for the first time on the relationships between Alsophila, Cyathea, and Gymnosphaera, i.e., Alsophila is sister to Gymnosphaera and then together as sister to Cyathea. As supported to be distinct from Alsophila in molecular phylogeny, in morphology, and in sporogenetic mechanism, Gymnosphaera is reinstated here, with a minor emendation in circumscription, as a separate genus. To facilitate the application of species' names and future revision, we provide a checklist of 43 taxa now known in Gymnosphaera with information of nomenclatural types and general distributions; among them 25 are new combinations.