Despite a significant body of evidence in support of the close phylogenetic relationship of species of Capronia (Herpotrichiellaceae) and black yeasts belonging to or allied with the genus Exophiala, questions concerning the taxonomic importance of features furnished by ascospore, stromal and anamorph characters have remained unanswered. In order to address these issues and to elucidate more fully relationships within the family, we have sequenced a portion of the nuclear large ribosomal RNA subunit (28S), the 5.8S gene, and the internal transcribed spacers (ITS1 and ITS2) of 15 species of Capronia and 19 black yeasts assigned to the form genera Cladosporium, Cladophialophora, Exophiala, Fonsecaea, Phaeococcomyces, Phialophora, Ramichloridium and Rhinocladiella. Cladistic analysis of these data confirmed the monophyly of the Herpotrichiellaceae but did not support the division of the genus Capronia on the basis of conidial ontogeny, pattern of ascospore septation, or the degree of stromal development. Homothallic species of Capronia with 8-spored asci, muriform ascospores and Exophiala anamorphs formed a well-supported lineage that included the medically important species Exophiala dermatitidis. Capronia mansonii and Capronia munkii, morphologically similar taxa isolated from the wood of Populus, were inferred as closely related but separate species. The clade comprising members of the Herpotrichiellaceae that possess Cladosporium-like and Phialophora anamorphs was also strongly supported. Available molecular evidence indicates that Dictyotrichiella semiimmersa and Phialophora americana are teleomorph and anamorph states of a single holomorph. Cladistic analysis also confirmed that the genera Cladophialophora and Ramichloridium are polyphyletic. The anamorphs of Capronia nigerrima and Dictyotrichiella semiimmersa are described and illustrated, and the combination Capronia semiimmersa is proposed.