The extant members of the earliest diverging pleurocarpous moss lineages comprise few species but span a wide range of structural and molecular diversity, most of it restricted to temperate and high-altitude tropical forests in the Southern Hemisphere. We present the most comprehensive molecular phylogenetic study of these lineages to date, based on parsimony and Bayesian analyses of four regions from the chloroplast and mitochondrial genomes. In addition to corroborating the findings of parsimony methods in this and previous studies, the results of heterogeneous Bayesian analyses provide strong support for sub-topologies that are also consistently found under parsimony, but are rarely well supported. Careful model specification and investigation of potential sources of error increase confidence in the Bayesian results, which provide the basis for a substantially revised classification reflecting the best currently available hypothesis of evolutionary history. The genera previously classified in the Rhizogoniaceae, together with Orthodontium, Orthodontopsis, Aulacomnium and Calomnion, are recognized in three families, the Orthodontiaceae, Rhizogoniaceae and Aulacomniaceae, and three monofamilial orders, the Orthodontiales ord. nov., Rhizogoniales and Aulacomniales ord. nov. Many of the species previously recognized in Hypnodendron are placed in Sciadocladus, Touwiodendron gen. nov., Dendro-hypnum or Mniodendron. These genera, with the exception of Sciadocladus, are placed in the Hypnodendraceae together with Spiridens, Franciella, Cyrtopus and Bescherellia. Braithwaitea is excluded from the Hypnodendraceae and recognized in the monogeneric Braithwaiteaceae fam. nov., while Sciadocladus is placed with Pterobryella and Cyrtopodendron in the Pterobryellaceae. The Hypnodendraceae, Pterobryellaceae, Braithwaiteaceae and Racopilaceae are recognized in the order Hypnodendrales comb. et stat. nov. We discuss the advantages and limitations of ranked classification systems and propose the abandonment of intercalated Linnaean ranks between order and class levels in Bryopsida. Three node-based informal names, the Pleurocarpids, the Core Pleurocarps and the Homocostate pleurocarps, are defined to represent evolutionarily significant clades within the pleurocarpous group.