The 18S rRNA gene sequences from the bitunicate ascomycetes Ceramothyrium linnaeae (Chaetothyriaceae) and Coccodinium bartschii (Coccodiniaceae) were determined and aligned with the corresponding sequences from 33 other ascomycetes and one basidiomycete, Boletus satanas. Phylogenetic analyses of these sequences supported previous reports that the Herpotrichiellaceae (Capronia, black yeasts, etc.) are distant from Dothideales and Pleosporales. A new sequence of Ceramothyrium linnaeae, representing the family Chaetothyriaceae, is monophyletic with representatives of the Herpotrichiellaceae, suggesting that both families can be accommodated in the order Chaetothyriales. The concept of Chaetothyriales can not be based on the presence of periphysoids, since Coccodinium bartschii, which also has periphysoids, clustered with members of the Dothideaceae. The Chaetothyriales are not closely related to other bitunicates, but are the sister group of either Eurotiales or Lecanorales/Peltigerales.