The current classification of Ascomycota is mainly based on nuclear SSU rRNA data. Most classes circumscribed in the filamentous Ascomycetes are based on nu SSU rRNA characters and morphology, but some groups, such as Lecanoromycetes have only low bootstrap support and the relationships of the classes is currently unresolved. To improve this, we used a multi-gene-approach including nu SSU-, nu LSU- and mitochondrial SSU-rDNA sequences of all traditionally (morphologically) distinguished and most recently accepted classes of filamentous Ascomycetes. Combined data sets were analysed phylogenetically using maximum parsimony and minimum evolution, and constrained topologies were tested with parametric bootstrapping. Most of these classes were found to be monophyletic with high bootstrap support. Lecanoromycetes showed a well-supported monophyly for the first time. The classification based on SSU rDNA data and different morphological characters, is supported, while the traditional classification and classifications based on the ascus-type are rejected. In contrast to single-gene-analyses also the branching order and relationships among these classes could partly be well-resolved. Our results suggest a basal position of the Dothideomycetes in the Leotiomyceta. Leotiomycetes and Sordariomycetes, as well as, Chaetothyriomycetes and Eurotiomycetes form well-supported clades.

Key words: Ascomycota, classes, fungi, molecular phylogeny, multiple-gene-analysis, nuclear SSU- and LSU- and mitochondrial SSU-rDNA