Lycophytes, comprising the groups historically known as the lycopsids and zosterophylls, have the longest history of any group of vascular land plants. The early evolution of the group is reviewed concentrating on the Late Silurian and Devonian record of Lycopsida and Zosterophyllopsida. Distinct root-like and shoot-like axes in zosterophyllopsids and lycopsids are first recorded in the Early Devonian and can be compared to the later development of pseudobipolar growth of tree-shaped lycopsids with upward-growing trunks and branch systems and downward-growing rooting systems. The development of stigmarian rootlets postdates the evolution of pseudobipolar growth, first recorded in the Middle Devonian, according to current evidence. Other important events in early lycophyte evolution during the Devonian include changes in leaf morphology, modification of sporophylls, and the eventual appearance of the lycopsid strobili.

The evolution of the isoetalean lycopsids spans much of the history of vascular plants, from Late, (or possibly Middle), Devonian to the current day genus Isoetes. The best known fossil members of this group are the arborescent lepidodendrids that dominated the Late Carboniferous coal swamps. Simpler unbranched isoetaleans with elongate stems also predated, coexisted with, and postdated the coal swamp trees, extending well into the Mesozoic. Whereas certain synapomorphies such as stigmarian rootlets, bipolar growth and secondary tissues unite the clade, other features characterize smaller subgroups of differing age, growth form and possibly, evolutionary lineage. Although some of these features are well known for plants of given time periods, particularly the Carboniferous, trends in character evolution have never been adequately documented for the group as a whole. A better understanding of such trends throughout the isoetalean fossil record could be valuable in distinguishing evolutionary lineages from convergence. It is interesting that several morphological characters of modern Isoetes are present as early as the Triassic: monolete microspores, sunken sporangia and elaborate ligules with glossopodia occur within elongate-stemmed Triassic forms. The dominant plant habit of modern Isoetes, a reduced cormose form that lacks appreciable stem elongation, originated at least by the Jurassic and typifies late Mesozoic and Cenozoic isoetaleans.

Two kinds of isoetalean lycopsids widely prevailed in the Triassic, the Pleuromeia-type and the Annalepis-type, the latter including a plexus of closely related genera. Comparative studies using new macromorphological and ultrastructural data suggest that both genera are interconnected and closely related to Isoetes. Morever they suggest that Annalepis is probably ancestral to Isoetes, via Isoetites. Besides several of the morphological and ultrastructural features of the Triassic lycopsids and Isoetes also appear to be present in some of the most ancient lycopsids, suggesting that the lineage including the modern Isoetales has a very remote origin.

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.

Despite its ancient origins, its worldwide distribution, and adaptation to diverse habitats, Isoëtes has a highly conserved morphology. This feature has made it difficult to resolve species and species relationships using morphological characters. In this paper, we report the utility of nucleotide sequences from the nuclear internal transcribed spacer (ITS) regions, chloroplast atpB/rbcL intergenic spacer region, and second intron of a LEAFY (LFY) homolog for identifying species relationships, delimiting basic diploid species, and determining hybrid origins. Variation in the ITS regions and atpB/rbcL spacer is most useful at the family level in Isoëtes and the LFY second intron is appropriate at the species and population level. The tree resulting from an analysis of the combined nuclear ITS and chloroplast atpB/rbcL spacer contains three major well supported clades (bootstrap ≥ 99%): an Old-World/California clade (I. abyssinica, I. longissima, I. velata, I. nuttallii, and I. orcuttii), an Asian/Australian clade (I. taiwanensis, I. japonica, I. kirkii, and I. drummondii), and a poorly resolved clade consisting of nine North American species. To further resolve and delimit the North American species, a combination of the LEAFY second intron and ITS data was used. The resulting consensus tree has limited resolution, supporting the hypothesis that the North American species complex radiated rapidly. The combination of LFY and ITS data provided numerous characters, both substitutions and indels, that are useful in species delimitation and identification of cryptic species. ITS sequence data, through additive banding and sequence misalignment, is also useful in confirming interspecific hybrids and determining their parental origins.