A series of phylogenetic analyses using nucleotide sequence data have resolved many aspects of the relationships in a group of land plants that until recently had received comparatively little attention, the homosporous lycopsids (Lycopodiaceae). The family includes no more than 400–500 living species but the group has evolved as an isolated lineage since the Early Devonian (390 Mya). Despite this ancient history, patterns emerging through the phylogenetic analyses imply that most diversification in this group is comparatively recent. The Lower Jurassic stem section Lycoxylon indicum indicates a minimum age for the split between Lycopodium and Lycopodiella at 208 Mya, and reticulate fossil spores from the Early Jurassic indicate that early cladogenesis in Lycopodium is of equivalent age. In the diverse predominantly epiphytic Huperzia group, biogeographic data indicates that 85–90 % of all living species result from cladogenic events postdating the final rifting of S. America and Africa in Mid to Late Cretaceous. The timing of these events coincides with the radiation of Angiosperms, and the diversification of epiphytic Huperzia was likely mediated by the development of broad leaved Angiosperm rain forests. Results indicate a single origin of epiphytism in Huperzia, but there have been at least two reversals to the terrestrial habit in the neotropics. The diversification of a large secondarily terrestrial clade, including about 80 montane high altitude species, was likely triggered by the Andean orogeny in the Mid Miocene, no more than 15 Mya.