The classification of the Bryopsida (mosses) has been based primarily on the variation of sporophytic characters i.e., architectural features of the peristome teeth that line the capsule mouth. Five arthrodontous peristome types have been recognized. Whether peristome types define natural groups and how they are evolutionary related has, however, remained unclear. Nucleotide sequence data from one nuclear and two chloroplast loci are generated and compiled to test two contrasting hypotheses regarding the ancestral peristome type in the Arthrodonteae. The genomic data partitions are incongruent with regard to the phylogenetic signal they carry. All phylogenetic analyses converge toward the polyphyly of the Funariineae and the Funariaceae. The Funariaceae are defined by the loss of a codon in therps4 gene. Goniomitrium acuminatum, the type of the genus, lacks this deletion, and is always resolved within the Haplolepideae. Consequently Goniomitrium is transferred to the Pottiaceae. The Ephemeraceae and Splachnobryaceae are tentatively retained as distinct, but with strong affinities to the Pottiineae. Neither the combined nor the independent data sets yield well supported topologies under the parsimony optimality criterion. Hence, the relationships among major lineages remain ambiguous. Inferences from chloroplast data alone yield a basal dichotomy between taxa with alternate peristomes (Orthotrichales and Bryales sensu lato) and those with opposite peristomes (Encalyptineae, Disceliaceae, Funariaceae, Timmiaceae, and the Haplolepideae). In contrast, analyses of the combined data resolve the Timmiaceae as sister to the split between the two peristomial lineages. It is hypothesized that the symmetric divisions of the IPL cells, is a synapomorphy for at least the Encalyptineae-Funariineae clade. The endostomial appendages of the timmiaceous peristome could, under either phylogenetic hypothesis, be regarded as homologous to the cilia in the bryoid peristome. Although the relationships among major lineages of arthrodontous mosses remain ambiguous, this study suggests that taxa with reduced or no peristomes, such as the Disceliaceae and the Gigaspermaceae, may be crucial in resolving the early evolutionary history of the Arthrodonteae when using DNA sequences.