Abstract:This experiment applies technique to analyze the polymorphism of the Fusarium strains. Using SDS alkaline lysis method extract the genomic DNA of eleven Fusarium which from the different part of Shanxi province. Amplifying the rDNA ITS region of these eleven Fusarium, which used one pair of differential primer, and betaken four restriction enzymes (TaqI, AluI, HaeⅢ, EcoRI) to digest the PCR amplification .Totally it gains sixteen polymorphic fragment which include eight special band, it’s molecular weight is 70-900bp. Finally adopted NTSYS-PC(2.1) package analyze the DNA restriction fragment polymorphism among every strains, which is classified five big groups and is coincident with the traditional classification. The result shows that this method can be used to analyze polymorphism among the Fusarium strains.