The perispore structure of Elaphoglossum was studied using a scanning electron microscope. Of the species examined, 119 corresponded to those used in a previously published phylogenetic analysis of the genus based on two chloroplast noncoding DNA regions, trnL-trnF and rps4-trnS. The spores of 102 additional species were examined for comparative purposes. Five perispore characters were scored for each species and optimized onto the previously published molecular tree. The morphology of the perispore and its character state changes are described and discussed in a phylogenetic context. Synapomorphies for major clades within the genus were identified, such as spines for the Neotropical species of sect. Squamipedia and perforations, spines, and cristae for subsect. Pachyglossa and a large subclade within sect. Setosa. This study is the largest done on perispore morphology in relation to phylogeny in a genus of ferns. Spore images of all species studied are available at http://www.plantsystematics.org.