The aim of the present paper is to investigate if Mycocalicium subtile as presently circumscribed is a morphologically highly variable species, or in fact represents two or more cryptic species, and further to investigate the status of M. minutellum. The morphological variation of 19 specimens of Mycocalicium subtile from five continents was investigated and the ITS1-5.8S-ITS2 region of their rDNA sequenced. Sequences from closely related taxa, 4 specimens of M. albonigrum, 2 of Mycocalicium sp., and Chaenothecopsis nana were also included. For comparison the corresponding sequence of M. victoriae and C. pusilla were also determined. We used the sequence of Monascus purpureus as the outgroup for the analysis. The sequences were used for phylogenetic inference using parsimony and distance methods. All the specimens assigned to M. subtile with the exception of two, form a well-supported monophyletic group. Those two specimens represent a morphologically cryptic, but genetically distinctive taxon. The infraspecific clades of M. subtile in the molecular phylogeny did not correspond to geographical origin. Only a weak correlation with geographical origin was found in the morphological analysis. The molecular analysis supports the suggestion that Mycocalicium minutellum is a taxonomic synonym of M. subtile.