The aim of the study is an expanded molecular phylogenetic analysis of the Holarctic taxa traditionally classified to the families Lophoziaceae, Scapaniaceae, Gymnomitriaceae and Jungermanniaceae. Also we will provide a justification of some nomenclatural changes suggested recently by Konstantinova & Vilnet (2009). The nuclear ITS1-2 and chloroplast trnL-F DNA sequences of 134 taxa (189 samples) from suborders Jungermanniineae and Cephaloziineae were analyzed. The topologies of phylogenetic trees constructed from combined sequences by maximum parsimony and Bayesian methods are congruent. The separation of family Diplophyllaceae from Scapaniaceae is not supported. The recently described family Solenostomataceae appears to be paraphyletic: the genus Nardia is in a sister relation to Gymnomitriaceae. The inclusion of the genus Isopaches in the family Anastrophyllaceae is questionable. Position of Obtusifolium and Protolophozia elongata in Scapaniaceae is not strongly supported. Phylogenetic relations within the genus Scapania are not fully resolved, but monophyly of sections Undulatae and Calcicolae is supported. Species assigned by some authors to a separate genus Scapaniella are scattered in different clades of the genus Scapania. Macrodiplophyllum imbricatum and M. plicatum can either be treated as Douinia or all these taxa included in Scapania. The distribution of species from the family Gymnomitriaceae on phylogenetic trees is congruent with the level of development or reduction of the perianth and perigynium. Taxonomically the species of Marsupella with reduced perianth are referred to Gymnomitrion, whereas the species called G. apiculatum that has a distinct perianth is transferred to Marsupella. The species status for Scapania tundrae, S. paludosa, S. crassiretis and Marsupella aquatica is supported. Genera Lophozia s.str., Schistochilopsis, Tritomaria, Protolophozia, Orthocaulis and Crossogyna are polyphyletic. The data support segregation of the recently described genera Pseudotritomaria, Heterogemma, Lophoziopsis, Pseudolophozia, Schljakovianthus, Schljakovia and Biantheridion.