Fusarium wilt of cotton, caused by the soil-borne fungus - Fusarium oxysporum formae specialis vasinfectum (Fov), is a worldwide disease of great economic importance. In Australia, it was first reported in 1993 in the Brookstead and Cecil Plans areas in the Darling Downs of Queensland (Kochman et al 1995). Now found in almost all major Australian cotton growing regions, Fusarium wilt has become a serious problem, causing substantial losses. Australian Fov strains have been demonstrated to be genetically distinct from all the overseas isolates screened to date (unpublished data). One possible explanation is that it is indigenous, previously occurring saprophytically in soil or parasitically on alternative hosts, and has recently arisen as a cotton pathogen as a consequence of unintentional selection for pathogenicity under cotton monoculture or host shifting. There are 17 native Gossypium species or wild cottons in Australia, four of which (G. australe, G. bickii, G. nelsonii, G. sturtianum) are widely distributed in the eastern and central areas where the major cotton-growing regions are located. As the closest relatives to the cultivated cottons, these native Gossypium species might have been associated with the Fov strains now present in the cotton-growing regions for a long period either by providing preferable habitats or acting as alternative hosts. In this study we aimed to determine whether there are any Fusarium wilt pathogens (Fov) occurring in association with these native Gossypium species. Furthermore, we also asked whether these native cottons are infected by other Fusarium species that in turn may be potential future threats to the cotton industry.