Contemporary taxonomists usually recognize a single species in Dumortiera, which is widely distributed through tropical and subtropical regions and extends into some temperate regions. Two subspecies, D. hirsuta subsp hirsuta and subsp. nepalensis, may be recognized, and both of these were thought to occur in Central America. We sequenced four loci, the nuclear internal transcribed spacer region ITS, and three chloroplast loci (rbcL, psbA-trnH and rpoC1) from 50 samples of Dumortiera across its geographic range to test for phylogenetic structure within the species and its congruence to morphological and geographic patterns. We also used light and scanning electron microscopy to examine morphological differences between accessions from Central America. Phylogenetic inferences reveal two highly distinct lineages: the first apparently restricted to Central America, and the second distributed across all the geographic regions sampled. This widespread lineage could itself be subdivided into several genetically and geographically distinct clades. The restricted Central American lineage contains plants that have a light green velvety appearance, due to an abundance of papillae on their upper thallus surface. These can therefore be distinguished morphologically from sympatric accessions of the widespread lineage, which are dark green, with a wide range of papillae densities (absent, few or abundant) on the thallus and usually with abundant marginal hairs. However, the wider application of these characters to lineages outside the Central American region has not yet been confirmed. We conclude that Dumortiera contains at least two, if not more, distinct species. The Asian epithet nepalensis does not seem applicable to plants in Central America, as the papillate morphotypes to which this name has been applied form an exclusively new world lineage. A thorough morphological revision of the genus, and reinvestigation of type material, is required.