The genus Orthotrichum Hedw. is one of the largest genera of mosses. Together with Ulota, Stoneobryum, Muelleriella and Orthomitrium it composes the Orthotricheae. Generic concepts in the Orthotrichaceae are based primarily on gametophytic features, whereas the infrageneric classification of Orthotrichum has traditionally relied almost exclusively on sporophytic features, and particularly the architecture of the peristome teeth and the degree of exposure of the stomatal guard cells. The classification of the Orthotrichaceae has recently been tested against a phylogenetic concept of taxa. This study revealed among others that species of Orthotrichum do not compose a monophyletic genus. Paraphyly is partially due to the recognition of oligospecific genera but also to the close affinities of some species of Orthotrichum to Ulota. Analysis of sequences of two chloroplast loci (trnL-trnF and rps4) obtained for nearly 80 exemplars of Orthotrichoideae lead to following results: Orthotrichum, and most of all speciose subgenera are para- or polyphyletic; Muelleriella , a genus of saxicolous subantarctic mosses is nested within a clade that can be defined by immersed vs. superficial stoma; subg. Orthophyllum is sister to the latter forming a lineage characterized by n=11 vs n=6. The hypotheses that diploidization and immersion of the stoma occurred twice in the Orthotricheae can be rejected. Similarly it is likely that dioicy is not a plesiotypic conditions, but rather evolved multiple times from monoicy. The loci sequenced hold about 10% parsimony informative characters and the trnL intron comprises about 20 unambiguous indels which define lineages within the clade of aneuploid taxa. Noteworthy is also the observation that the doubling of chromosome number is accompanied by a conspicuous acceleration of the rate of molecular evolution.

Key words: Bryophytes, cytology, Orthotrichum, phylogeny, rps4, trnL