A preliminary phylogenetic analysis is presented for Lomariopsis based on sequence data from the chloroplast intergenic spacer trnL-trnF. The analysis includes 27 (60%) of the approximately 45 species in the genus. A strict consensus of six most parsimonious trees supports two main clades—the Sorbifolia-group and the Japurensis-group—previously proposed based on heteroblastic leaf development. The Sorbifolia-group is entirely neotropical and includes all the Antillean species. The species in this clade had either smooth or crested spores, but the tree was ambiguous whether these spore types define two separate clades. The Japurensis-group consists of two clades, one primarily neotropical and the other entirely paleotropical. Within the neotropical clade nests a clade of two African species, which have long-spiny spores typical of the neotropical clade and unlike those found in the African-Madagascan clade. The occurrence of these two species in Africa is best explained by long-distance spore dispersal of their ancestral species from the neotropics to Africa. Within the paleotropical clade of the Japurensis-group, a clade of three African species is nested among seven species from Madagascar (all the species from that island). Within the genus as a whole, a derived character—the abortion of the rachis apex and its replacement by the distal lateral pinna assuming a terminal position—was found to have evolved separately in each of the four species with this kind of leaf apex. A scanning electron microcope study of the spores revealed five types, and a transformation series for these different types is proposed. Characters of spore morphology and heteroblastic leaf development agreed with many of the clades in the phylogenetic tree. This study represents the first phylogeny for the genus.