Penicillium brevicompactum and other isolates with the compact, complex conidiogenous apparatus typical of the species were sequenced in one ribosomal and two protein coding regions. The aligned DNA sequences were analyzed by maximum parsimony and the data from different loci were tested for compatibility using the partition homogeneity test. Analysis of each of the three loci revealed three clades corresponding to P. brevicompactum, P. olsonii and P. biourgeianum. Using the phylogenetic species concept and the genetic isolation of the clades, P. hagemi, P. patrismei, P. stoloniferum, and P. griseobrunneum are all synonyms of P. brevicompactum. P. volgaense is a synonym of Penicillium olsonii, while P. biourgeianum is a distinct species closely related to P. brevicompactum and P. olsonii. Phenotypic distinctions between the species are mostly based on colony characteristics such as colour. P. bialowiezenze, often treated as a synonym of P. brevicompactum, is most closely related to P. polonicum.