We analyzed nucleotide variation in rbcL (the gene encoding the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase) from 99 genera of leptosporangiate ferns representing 31 of the 33 extant families. Phylogenetic relationships were inferred using three methods: neighbor joining, maximum parsimony, and maximum likelihood. All three methods resulted in optimal trees that were similar. Within the context of those taxa examined, these trees suggest that: 1) Polypodiaceae, Grammitidaceae and Pleurosoriopsis form a monophyletic group that is most derived among indusiate ferns; 2) Davallia is closely related to the Polypodiaceae; 3) Tectaria is related to Oleandraceae rather than to other members of Dryopteridaceae; 4) Rumohra and Elaphoglossum are closely related; 5) Dryopteridaceae are polyphyletic; 6) a monophyletic group consists of Polypodiaceae, Grammitidaceae, Davalliaceae, Oleandraceae, Nephrolepidaceae, Lomariopsidaceae, Dryopteridaceae, Thelypteridaceae, Blechnaceae, Aspleniaceae, and Pleurosoriopsis; 7) Dennstaedtiaceae, Monachosoraceae, Pteridaceae, Vittariaceae, and the previous clade form a monophyletic group; 8) Dennstaedtiaceae are polyphyletic; 9) tree ferns in the Cyatheaceae, Metaxyaceae, and Dicksoniaceae form a monophyletic group that emerged early in the diversification of leptosporangiate ferns; 10) Plagiogyriaceae and Loxomataceae emerge with the tree ferns; 11) heterosporous water ferns form a monophyletic group that diverged prior to the tree ferns; 12) Schizaeaceae, Cheiropleuriaceae, Dipteridaceae, Gleicheniaceae, Matoniaceae, and Hymenophyllaceae are basal to the heterosporous aquatic ferns; and 13) Osmundaceae are the most basal lineage of the leptosporangiate ferns.