An overview of current phylogenetic studies employing molecular data to test previously formulated hypotheses of relationships of loculoascomycetes and pyrenomycetes is given, concentrating on three topics: (1) circumscription and classification of loculoascomycetes, (2) a new classification of Sordariales, and (3) the phylogenetic occurrence of lichenized pyrenomycetes. With regard to these three examples, our review indicates: (1) In traditional taxonomy ascomycetes were classified according to their ascoma-types, with the class Pyrenomycetes including all taxa having perithecia. Later, the development of ascomata and the type of ascus were employed for higher-level classification, and consequently, Loculoascomycetes was separated from Pyrenomycetes. However, molecular studies show that even these revised classifications were too coarse. The Loculoascomycetes fall into two distinct and not closely related groups, which are placed in two clades: Chaetothyriomycetidae and Dothideomycetes. (2) Ascospore morphology has been widely used in taxonomy of ascomycetes, and Sordariales is a prominent example of this. Molecular data suggest that ascomatal wall morphology is a better predictor of phylogenetic relationships in these fungi. Further, the molecular data helped to redefine the circumscription of Sordariales. (3) The majority of non-lichenized pyrenomycetes form a monophyletic group: Sordariomycetes. However, the lichenized pyrenomycetes are highly polyphyletic. Pyrenocarpous lichen-forming fungi occur in several lineages each in Dothideomycetes, Chaetothyriomycetidae, and Lecanoromycetes, whereas no lichenized forms are currently known in the classical pyrenomycetous Sordariomycetes.