Phylogenetic analysis of nucleotide sequences of chloroplast rDNA internal transcribed spacer (cpITS) regions (cpITS2-4) of 14 species of liverworts, 4 species of hornworts, 20 species of mosses, 7 species of lycopods and 2 species of algae was carried out. Phylogenetic trees constructed by maximum parsimony, maximum likelihood and neighbour-joining methods indicated that bryophytes are not monophyletic. The cpITS data suggest that the hepatic lineage branches most deeply in the land plant topology and that mosses are monophyletic, forming the sister group of lycopods and hornworts. Within the mosses, a conspicuous deletion with distinct phylogenetic distribution was observed in the cpITS3 region. This deletion is absent in other land plants, including the enigmatic genus Takakia, and marks Takakia as an evolutionary lineage distinct from mosses.