Random amplified polymorphic DNA markers were characterized for three taxonomically problematic Penicillium species: P. aurantiogriseum var. aurantiogriseum, P. verrucosum and P. puberulum, as well as for 25 species of mono-, bi-, and terverticillate Penicillia. The relationship of P. vulpinum with bi- and terverticillate Penicillium species was investigated and genetic relationships among mono, bi-, and terverticillate Penicillium species were determined from these RAPD markers. Eight species from mono-, eight from bi-, and nine from terverticillate Penicillia were examined. With 14 randomly chosen 10-mer primers, a 310 character by 25 species matrix was generated. Phenetic analysis separated the 25 species into three genetically distinct groups that correspond to the different arrangements of penicilli (mono-, bi-, and terverticillate). The results of this study suggest that P. aurantiogriseum var. aurantiogriseum, P. verrucosum, and P. puberulum represent genetically distinct species, and that P. vulpinum should be included in terverticillate Penicillia Phenogram branching patterns indicated that biverticillate species are genetically more similar to monoverticillate species than they are to terverticillate species.