To clarify the genetic difference and phylogenic relationship among the strains of Fusarium oxysporum, the genetic diversity of 33 F. oxysporum strains from different geographic origin was examined by inter-simple sequence repeats (ISSR). A total of 105 bands were amplified with 11 selected ISSR primers, 91 (86.7%) of which were polymorphic. The cluster analysis based on the ISSR data showed that the genetic similarity among the strains ranged from 0.606 to 0.962, with an average of 0.756, and all the strains could be distinguished at 0.962, which indicated that the SSR loci in F. oxysporum genomes were rich in polymorphism. There existed definite correlations between the genetic similarity and geographic origin of the strains isolated from the same hosts.