Basal mosses are stable at the base of phylogenetic trees. Although they are a small part of mosses (10 families in 7 classes and 2 subclasses), they receive considerable attention because of their abundant morphological variations and importance in resolving the phylogeny of Bryophyta. We used maximum likelihood, Bayesian analysis and most parsimonious methods with data for 9 regions (26S, 18S, nad5, cox1, rbcL, rps4, cp-LSU, cp-SSU, atpB) to estimate the phylogenetic relationships of 48 species (36 mosses, 4 tracheophytes, 2 hornworts, 4 liverworts and 2 algaes). We resolved the previous incongruence among basal mosses and provide strong support for previous resolutions. The phylogenetic tree with high statistical support showed that (1) Takakiopsida and Sphagnopsida form a sister group at the base of the moss linage; (2) Andreaeopsida is sister to Andreaeobryopsida; (3) Oedipodiopsida forms a sister group with all the peristomate mosses; (4) Tetraphidopsida is sister to the clade unifying Polytrichopsida and Arthrodontous taxa; and (5)Buxbaumiidae is at the base of Bryopsida, followed by Diphysciidae.