Nucleotide sequences from the trnL-F spacer region and the rbcL region of the chloroplast genome were used to resolve subgeneric relationships within Elaphoglossum. Fifty-four representative species from the nine sections, as defined by Mickel and Atehortua, and six species from outgroup genera Lomariopsis, Bolbitis, Rumohra and Athyrium were sequenced for the trnL data set and about half were included in the rbcL data set. The genus Elaphoglossum is one of the largest and most complex of fern genera, composed of over 600 species which are nearly all simple-bladed with acrostichoid sori. The majority of useful taxonomic characters to date have been vegetative ones, especially those of the scales and blades. Results from this study support the use of these characters for definition of the sections and in general support the definition of the sections outlined by Mickel and Atehortua. However, new observations from this analysis indicate that there is strong support for three clades within the section Pachyglossa and that the subsection Squamipedia is more distinct than suspected. All species with resinous dots fall within the same section; there is no support for maintaining Decorata as a separate section; and the section Amygdalifolia remains unique indicating there may beat least two origins of hydathodes.

Key words: Elaphoglossum, fern, phylogeny, rbcL, trnL