Elaphoglossum is comprised almost entirely of epiphytic species with simple and entire leaves. Elaphoglossum section Squamipedia is intriguing because four of its species have dissected leaves. To generate a phylogenetic hypothesis of the relationships among all taxa belonging to section Squamipedia, we assembled a three-locus plastid dataset that included all recognized species in the section plus taxa representing all other sections of Elaphoglossum and three bolbitidoid genera. Our results support section Squamipedia as monophyletic. The species belonging to section Squamipedia are recovered in two well supported clades. The first clade includes two species endemic to Madagascar, whereas the second includes 16 species endemic to the Neotropics. Echinulate spores are synapomophic for the Neotropical species of section Squamipedia. Other characters that characterize most species of section Squamipedia are long-creeping rhizomes and absence of phyllopodia; however, two species of section Squamipedia (E. nidusoides and E. nidiforme) have phyllopodia and short-creeping rhizomes. The four species with dissected leaves belong to different clades and had independent origins from ancestors with simple, entire leaves. Dissected leaves have evolved at least six times during the history of Elaphoglossum. Elaphoglossum lloense and E. squamipes, two species defined on the basis of morphology, are not supported by our molecular analyses, being recovered in three and two different clades, respectively.