This paper summarizes the applications of modern biological technology, such as vegetative compatibility groups (VCG), restriction fragment length polymorphisms (RFLP) and inter-simple sequence repeat (ISSR), rDNA-ITS, translation elongation factor1-α (EF-α) sequence analysis in the research of classification system and an identification method of Fusarium, and obtains molecular biology such as RFLP and ISSR were used to analysis the correlation between individuals and geographical origin strains, rDNA-ITS, EF-α sequence analysis had provided the basis for classification and identification about Fusarium at the level of species and subspecies, the VCG was used for distinguish different genetic structure of the group that lack teleomorph. The future direction was discussed.