Phylogenetic relationships among genera of the Ophioglossaceae are controversial because morphological/anatomical features have been interpreted differently by various researchers. To construct a phylogeny of the family, I sequenced the protein encoding gene rbcL and the non-coding spacer region trnL-F from approximately 40 species representing the range of diversity of the family. In addition, I analyzed cladistically morphological/anatomical characters from the same taxa to provide an independent comparison to the molecular phylogeny. All three data sets supported two major clades within the family, an ophioglossoid lineage and a botrychioid lineage. Helminthostachys is sister to a monophyletic Botrychium s.l., in which Botrychium s.s. is sister to Sceptridium, and Botrypus is paraphyletic. Though relationships within Ophioglossum s.l. were not well resolved, Cheiroglossa and Ophioderma appear to be sister taxa, and Ophioglossum s.s. may be paraphyletic.

Key words: Botrychium, Helminthostachys, Ophioglossaceae, Ophioglossum, phylogeny