Fusarium oxysporum f. sp. vasinfectum (Fov) is an economically significant pathogen of cotton in Australia. Although the levels of resistance present in the new commercial cultivars have significantly improved, cotton breeders continue to look for additional sources of resistance. The native Australian Gossypium species represent an alternative source of resistance because they could have co-evolved with the indigenous Fov pathogens. However, they belong to the tertiary germplasm pool, which is the most difficult group of species from which to introgress genes into cultivated cottons. Interspecific triploid hybrids can be generated but they are sterile. The sterility barrier can be overcome using synthetic polyploids as introgression bridges, but it now clear that there is insufficient homoeologous chromosome interaction at meiosis to make these good breeding lines. A careful analysis of these lines, however, provides, an opportunity to begin to understand the genetics of fusarium wilt resistance in cotton. Fov disease bioassays on G. hirsutum X G. sturtianum BC3 multiple alien chromosome addition lines revealed that two G. sturtianum linkage groups were associated with improved Fov resistance, while two G. sturtianum linkage groups were associated with increased Fov susceptibility. This result suggests many genes are interacting in the cotton plant to determine the level of fusarium wilt resistance. To complete our understanding of the complex inheritance of resistance to the fusarium wilt disease in cotton, quantitative trait loci analyses of the segregation of fusarium wilt resistance in an elite cotton family have been undertaken. We aim to map quantitative disease resistance loci, which act additively to confer disease resistance against Fusarium wilt. By identifying QTLs for fusarium wilt resistance, we intend to identify the genes involved and mark them with molecular marker surrogates that can be used in marker assisted breeding projects to develop a new generation of better fusarium wilt resistant cultivars.