Relationships between Scopulariopsis species and allied fungi were studied by sequencing a 350 bp gene region of the large subunit ribosomal RNA gene (LSU rDNA). In addition, a limited morphological dataset of nine characters was included in the cladistic analysis. Nineteen mitosporic strains (nine Scopulariopsis, five Wardomyces, three Doratomyces, one Trichurus and one Scedosporium species) and 21 meiosporic strains (14 Microascus, 4 Kernia and 3 Pithoascus species) were studied. The data were analysed using parsimony methods. Based on the analyses, the studied microascaceous fungi are divided to 12 molecular lineages. Most of the opportunistic human pathogenic Scopulariopsis species are placed in one clade ('Microascus manginii Clade'). Most synnematous anamorphs with Scopulariopsis-like conidia (Doratomyces and Trichurus) are placed in another clade ('Microascus albonigrescens Clade'), together with Wardomyces. Microascus sensu lato can be divided into seven clades which also incorporate all studied Pithoascus, Scopulariopsis, Wardomyces and Trichurus species and most of the Doratomyces species. Most of the Kernia teleomorphs and one Doratomyces species are placed in a different main clade, together with Pseudallescheria and Petriella. Future alternatives in the taxonomy of Microascus include splitting the genus or redefining it to include deviating taxa. More molecular data need to be obtained and considered in either case.