Gene sequence data have been newly obtained for 18 species in 13 genera of the order Nemaliales (Rhodophyta), allowing for the first time a relatively comprehensive molecular phylogenetic appraisal of the order. The phylogenetic trees generated from these data support the recognition of three families: (i) the Liagoraceae as presently constituted; (ii) a reduced Galaxauraceae including Actinotrichia, Galaxaura (sensu lato), and Tricleocarpa; and (iii) a new family, Scinaiaceae, segregated from the Galaxauraceae and including the genera Scinaia, Gloiophloea, Nothogenia, and probably Whidbeyella. The four genera of the Scinaiaceae differ from the newly circumscribed Galaxauraceae in being uncalcified, and having heteromorphic life histories in which the tetrasporophyte is much reduced and filamentous or crustose. This type of life history is found in only Tricleocarpa of the Galaxauraceae. The results also show Galaxaura to be para/polyphyletic if Actinotrichia and Tricleocarpa are recognized. To remedy this, the Galaxaura marginata species complex, Galaxaura diesingiana, and Galaxaura obtusata are removed from the genus and placed in the resurrected Dichotomaria Lamarck. Galaxaura marginata, presently thought to be wide-ranging and morphologically variable, is shown to comprise several species. As a consequence, Galaxaura tenera Kjellman and Brachycladia australis Sonder are removed from the synonymy of G. marginata and restored as independent species in Dichotomaria for South African and Australian isolates, respectively. The Liagoraceae is shown to encompass genera previously placed in the segregate families Nemaliaceae and Dermonemataceae, and the value of the reproductive characters used to define those taxa is discussed.