Technical Abstract: The members of the Aspergillus section Nigri, known as black-spored aspergilli, can contaminate several substrates including maize. Although some species within the group can produce plant disease symptoms such as black mold in onions and maize ear rot, the main concern with A. niger aggregate contamination is the production of a chlorinated cyclic polyketide, ochratoxin A. This mycotoxin is nephrotoxic, teratogenic, and carcinogenic to animals. The accurate classification and identification of ochratoxigenic fungi is relevant since it is not clear which strains within A. niger aggregate are capable of producing ochratoxin A on maize and maize products. However this task has been difficult because the morphology of most of the members is very similar. In order to differentiate species within this aggregate we report the use of a repetitive-sequence-based DNA fingerprinting method that looks promising. We used 27 Aspergillus section Nigri species and strains that were previously identified by microscopy and our results indicated a high concordance between the automated DNA fingerprinting system and morphology. This technique reduces the time required by other molecular methods.