The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.