Traditional taxonomy of aquatic hyphomycetes has been based on conidial morphology and development. Since the predominantly tetraradiate and sigmoid forms are due to convergent evolution, they are often phylogenetically non-informative. The comparison of nuclear small-subunit ribosomal DNA sequences of 30 species (22 new, eight previously published) assigned 22 to Leotiomycetes, four to Dothideomycetes, three to Sordariomycetes, and one to Orbiliomycetes. Eight species of Anguillospora were distributed among the Leotiomycetes, Dothideomycetes, and Orbiliomycetes. All three anamorphs connected with Massarina were assigned to the Pleosporales, however, Clavariopsis aquatica and Tumularia aquatica separated from Anguillospora longissima. The nSSU rDNA sequences of several species were identical (e.g. Anguillospora crassa and A. furtiva), suggesting the need to include less conservative genes for resolving such differences.