Fusarium spp. produce fumonisin, fumonisin consider one of the mycotoxin groups that contaminate feed and food products and posses maximum threat to human and animal health. Twelve Fusarium isolates were isolated from four Egyptian governorates, i.e, Kafrelsheikh, Dakahlia, Gharbia and Behera. One isolate (F. verticillioides) from infected corn, 10 isolates from infected rice with bakanae disease (F. moniliforme) and one F. solani isolate from infected wheat. Two specific primers named VERTF-1 and FUM1 were used in this study to PCR assay to discriminate fumonisin producing and non producing strains. The Inter Generic Spacer region (IGS) of rDNA coding units and polyketide synthase (PKS) gene FUM1. Eleven isolates were positive for VERTF-1 primer and proved to be potential fumonisin producers and one isolate (Fusarium solani) was scored negative for both primers. The primer FUM1 showed negative signal in five strains, one of F. verticillioides and five of Fusarium moniliforme. This present study provide quite rapid and specific method helps in accurate discrimination of fumonisin producing strains.