Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon
sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for
three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate
ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent
phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the
five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses.