Technical Abstract: Some species in the Aspergillus section Nigri, are known for their production of mycotoxins, including ochratoxin A, a chlorinated cyclic polyketide compound. Ochratoxin A has been classified as possible carcinogenic to humans by the International Agency for Research on Cancer, and the evidence suggests nephrotoxic, teratogenic and carcinogenic activities in laboratory animals. The accurate classification and identification of ochratoxigenic species within the A. niger aggregate has been elusive since the morphology of most of the member is very similar. Molecular biology techniques have been developed in order to differentiate species within this aggregate, however most of them are impractical for routine identification and they required too much time. In this work, we report the use of an automated repetitive-sequence-based DNA fingerprinting method which reduces the time and labor required by other molecular methods. 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.