The fungi Fusarium oxysporum f. sp. vasinfectum (Fov) and F. oxysporum f. sp. phaseoli (Fop) are important pathogens that cause wilt on cotton and common bean, respectively. In the present study, phylogenetic trees constructed with partial sequences of the translation elongation factor gene and ribosomal intergenic spacer region of Brazilian Fov and Fop strains revealed polyphyletic origin of strains within both formae speciales. This creates an obstacle for the development of specific molecular diagnostic methods and explains the failure of supposedly specific methods described in the literature to correctly discriminate formae speciales of F. oxysporum.