The study on molecular structure of Fusarium proliferatum clinically isolated can provide the basis for accurate diagnosis and treatment of F. proliferatum infection. The rDNA ITS gene of 6 strains that had been identified as Fusarium proliferatum based on morphological were cloned and sequenced. The molecule phylogenetic tree was constructed based on rDNA ITS sequences, and the 6 genus were divided into two groups. Group I was F.proliferatum, including strains of CSUFT201, CSUFT204, CSUFT205. Group II was F. moniliforme, including CSUFT202, CSUFT203, CSUFT206. The results of this study showed that 3 strains of F. moniliforme were confirmed out of the 6 strains with the molecular methods.