Genetic diversity for traits such as fibre quality or disease resistance to microorganisms is limited in the elite cotton germplasm; consequently, cotton breeders are looking for novel alleles in the secondary or even in the tertiary gene pools. The wild Australian Gossypium species (tertiary gene pool) represent an alternative source of novel alleles. However, to use these species efficiently, enabling tools are required. Chromosome-specific molecular markers are particularly useful tools to track the transmission of this exotic genetic material into the cultivated cotton during introgression. In this study, we report the construction of a genetic linkage map of the Australian wild C-genome species Gossypium sturtianum. The map, based on an F(2) population of 114 individuals, contains 291 AFLP loci. The map spans 1697 cM with an average distance of 5.8 cM between markers. To associate C-genome chromosomes with the A and D subgenomes of cultivated cotton, 29 SSR and RFLP-STS markers were assigned to chromosomes using cultivated cotton mapped marker information. Polymorphisms were revealed by 51 AFLP primer combinations and 38 RFLP-STS and 115 SSR cotton mapped markers. The utility of transferring RFLP-STS and SSR cotton mapped markers to other Gossypium species shows the usefulness of a comparative approach as a source of markers and for aligning the genetic map of G. sturtianum with the cultivated species in the future. This also indicates that the overall structure of the G. sturtianum linkage groups is similar to that of the A and D subgenomes of cotton at the gross structural level. Applications of the map for the Australia wild C-genome species and cotton breeding are discussed.