Abstract: To explore the phylogenetic correlations among the strains of Fusarium spp., the mitochondrial small subunit (mtSSU) rDNA genes from Fusarium oxysporum f.sp.cubense in two physiological races (race4 and race1) were amplified by polymerase chain reaction using the mtSSU rDNA gene universal primers. Furthermore, phylogenetic tree was constructed on the basis of the two race mtSSU rDNA sequences and other mtSSU rDNA sequences of Fusarium spp. from GenBank by neighbor-joining method. The results showed that lengths of the gene in two races were 685bp and sequence homology between the two races was 99.70%. Phylogenetic analysis suggested that the two sequences were clustered in the same group with the sequence of F. oxysporum f.sp.cubense in the database. Meanwhile, there were variations in the mtSSU rDNA sequences of inter-species and the same species with different specialized obviously, suggesting that the abundant genetic diversity of mtSSU rDNA gene sequences could be used in phylogenetic and evolutionary analyses of Fusarium spp.