Notwithstanding significant progress in our understanding of the relationships of basal pteridophytes, the phylogeny of derived leptosporangiate ferns, the Polypodiales, remains enigmatic. Although demonstrably monophyletic, the deeper branching patterns within the group remain uncertain and highly controversial. Accordingly, I conducted an analysis of 40 genera representing each major lineage of Polypodiales based on a combination of three molecular data sets (rbcL, rps4 and nad5). Although results are preliminary in view of limited taxon sampling, several interesting observations emerge. The basal position of the dennstaedtioid ferns is unperturbed. From this group a monphyletic clade of pteridoid ferns is derived, characterized by the loss of a true indusium and the migration of sporangia back from the laminar margin along the veins. Also derived from this group is an as yet unnamed monophyletic clade of ferns in which the indusium is retained but which is also characterized by a migration of the sorus from a marginal to medial position. The indusiate clade is divided into an asplenioid group and an unnamed sister group that is further divided into two unnamed groups, each with good phylogenetic support. The first group is characterized by the presence of mostly linear, indusiate sori; a fundamentally terrestrial habit; and often strongly dimorphic leaves. The second group is characterized by having round sori, which in several subclades become exindusiate; a more or less epilithic to epiphytic habit; and monomorphic leaves in basal clades which often become strongly dimorphic in epiphytic lineages. The relationship of groups within the second clade suggests a directed diversification related to increasing specialization for the epiphytic habit, while epiphytism is absent from the first clade entirely

Key words: evolution, nad5, Polypodiales, pteridphyte phylogenetics, rbcL, rps4