Molecular analysis and experimental inoculations showed Fusarium oxysporum f. sp. vasinfectum (FOV) and F. redolens as the causal agents of wilting of cotton in Iran. Twenty-seven Fusarium isolates were obtained from necrotic and discolored root and crown tissues of cotton in Iran. Morphological features and molecular analysis with species-specific primers showed that 20 isolates belonged to FOV race 3 and F. redolens. Phylogenetical analysis based on translation elongation factor-1α (tef1) sequences dataset clearly classified 7 Iranian FOV genotypes in race 4, 7 or 8 group. In addition, molecular study and pathogenicity tests showed that F. redolens, like FOV race 3 genotype, also caused discolorations on the root and crown of cotton.