The main goal of this work was to develop rapid and accurate molecular tools to discriminate species of white industrial Penicillia. We applied three different polymerase chain reaction (PCR) based techniques. Sequences of the ITS region of the rRNA gene unit and of the 5' end of the beta tubulin gene yielded 1.2% and 5.8% nucleotide variability respectively, between Penicillium camembertii and Penicillium nalgiovense. Polymorphic restriction sites were found in both sequences. These may be used in diagnostic PCR-RFLP analysis to rapidly distinguish between the two Penicillium species. Random amplified polymorphic DNA (RAPD) markers were also useful to differentiate these two species, but no polymorphism was found at the subspecific level, which evidenced a high level of homogeneity of the isolates studied. By means of these three techniques, the real identity of industrial strains of Penicillium chrysogenum and P. nalgiovense could be demonstrated. The comparison of these isolates with type strains of the two species suggested that the former corresponds to P. nalgiovense. The genetic relatedness between P. naglovense and Penicillium dipodomyis was also confirmed.