Aspergillus niger is a significant component of the fungal community on grapes. The mycotoxin fumonisin B2 (FB2) was recently detected in grape must and wine as well as in cultures of some A. niger strains isolated from grapes and raisins. This study examined 48 strains of Aspergillus section Nigri for the presence of the fumonisin biosynthetic gene fum8 in relation to FB2 production. The fum8 gene was detected in only 11 A. niger strains, 9 of which also produced FB2. Maximum parsimony analysis based on the calmodulin gene sequence indicated that the presence/absence of fum8 is not correlated with the phylogenetic relationship of the isolates. This is the first report correlating the presence of a fumonisin biosynthetic gene with fumonisin production in A. niger from an important food crop. The results suggest that the absence of FB2 production in grape isolates of A. niger can result from the absence of at least one gene essential for production.