The genome of Aspergillus niger (MPS-002) was subjected to RAPD fingerprinting using none different random oligonucleotide primers. A 0.7 Kb PCR amplicon, generated by primer-3 could be used as a RFLP probe to differentiate A. niger (ATCC 16880) from A. niger (MPS-002). The probe revealed DNA polymorphism internal to two different EcoRI recognition sequences spaced apart at a distance of 0.4 Kb within a 4.0 Kb EcoRI fragment of the genome of both the strains. Localized genome mapping analysis further revealed that the 0.7 Kb RFLP probe was positioned at a distance of 2.7 Kb and 0.6 Kb from the two ends of a 4.0 Kb EcoRI fragment, respectively within the genome of the two strains of A. niger. (c) 2005 Elsevier Ltd. All rights reserved.