The nucleotide sequences of the genes encoding the 18S rRNA of Aspergillus flavus, A. nidulans, A. terreus and A. niger were elucidated and aligned to the sequences of A. fumigatus. In addition, the 18S rRNA sequences of the V4-V9 region of morphologically similar filamentous fungi, e.g. Penicillium chrysogenum, P. marneffei and Paecilomyces variotii, were elucidated. Phylogenetic analysis and comparison showed a very close intergeneric relationship of the genus Aspergillus to species of the genera Paecilomyces and Penicillium. However, the sequenced Aspergillus species also showed a very close relationship to Eurotium rubrum and Monascus purpureus. Phylogenetic analysis of fungal 18S rRNA sequences divided the general Aspergillus, Penicillium and Paecilomyces into two coherent clusters and showed a close intergeneric relationship which is in keeping with the existing morphological and taxonomic classification.