The food-borne fungus Neosartorya fischeri, which is phenotypically related to the human opportunistic pathogen Aspergillus fumigatus, causes spoilage of heat-processed fruit products. Genomic methods were used to type N. fischeri strains and identify the genomic relationship between A. fumigatus and N. fischeri and between the different varieties of N. fischeri. EcoRI restriction fragment length polymorphism (RFLP) patterns obtained after ethidium bromide staining could differentiate most of N. fischeri var. glabra and N. fischeri var. spinosa strains. On the contrary, all N. fischeri var. fischeri strains tested exhibit the same RFLP pattern, which was similar to the A. fumigatus pattern. Similarly, Southern hybridization with a ribosomal probe showed some polymorphism between N. fischeri var. glabra and N. fischeri var. spinosa strains but could not distinguish between N. fischeri var. fischeri and A. fumigatus strains. By using the endonucleases EcoRI, HindIII, and BglII to generate Southern blot patterns with a fragment of the A. fumigatus gene coding for a 33-kDa protease, it was possible to differentiate N. fischeri var. fischeri from A. fumigatus. The difference between N. fischeri and A. fumigatus was confirmed by the use of moderately repetitive nonribosomal A. fumigatus sequences. These results are in agreement with previous studies that showed important infraspecific polymorphism within N. fischeri var. glabra and N. fischeri var. spinosa and, in contrast, the homogeneity of N. fischeri var. fischeri strains. A unique Southern blot pattern was seen for each strain of N. fischeri fingerprinted with the A. fumigatus repetitive sequence.(ABSTRACT TRUNCATED AT 250 WORDS)