Although considerable progress has recently been made in the phylogeny of Hymenasplenium, the genus remains poorly investigated; specifically, the diversification and historical biogeography of the genus have been little studied. Here, we infer an updated plastid DNA phylogeny and the first large-scale nuclear DNA phylogeny to understand the biogeography of the genus. The plastid phylogeny includes 312 accessions from across the genus ' distribution range (ca. 121% increase of the latest sampling), with special attention paid to island accessions from 14 Indian Ocean and Pacific islands, whereas the nuclear phylogeny includes 161 accessions of the Afro-Eurasian species. We identify one new major clade and two new subclades. Reticulate evolution was revealed both among subclades and among species in the Afro-Eurasian. Our divergence-time analyses show that most of the extant species diversity has arisen from diversification after the Oligocene despite a Cretaceous origin of the genus. Ancestral area reconstruction revealed that vicariance likely played a major role in building biogeographic patterns at deep evolutionary scales (the Afro-Eurasian clade and the American clade) in Hymenasplenium, while the intercontinental disjunctions within the Afro-Eurasian clade among Asia, Africa, and Oceania might have resulted from frequent long-distance dispersal events from Asia to Oceania and Africa.