Abstract: This experiment take the PMD18-T as the vector, expanding and sequencing the ITS and 28S partial sequences of ten Fusarium strains, utilizing the DNAMAN4.0 software to do analyzing of the multiple sequence and the genetic distance, establishing the molecular system evolution tree. The result indicates that the genetic relationship of each strains between the 92.2% to 99.9%, reflect the inter-species have bigger genetic diversity, This is coincide with the different kind species which is appraised by the morphology analysis, but the same species which are different specialized types and biological races from the different area or host which have the higher homology about between 96.6% to100%. This indicates that the genes of rDNA of the same species which are different specialized types and biological races are higher homology. It is possible that they haven’t difference or the difference is very small.