RAPD (random amplified polymorphic DNA) markers generated by 30 random decamer primers were used to fingerprint 12 released cultivars and a breeding line of Gossypium hirsutum and 1 cultivar of G. barbadense presently under cultivation in Australia. Among a total of 453 developed markers, 69 (15.2%) were only present (unique) in the G. barbadense cultivar Pima S-7. Of the remaining markers, 128 (33.3%) were fixed in all 13 G. hirsutum cultivars. In pairwise comparisons of the degree of band sharing, nine closely-related cultivars showed 92.1-98.9% genetic similarity. Cluster analysis of genetic distance estimates between each of the cultivars revealed phylogenetic relationships in broad agreement with the known lineage of the cultivars. Ten of the G. hirsutum cultivars can be characterized individually based upon cultivar-specific RAPD markers, thus making it possible to differentiate closely related cultivars by molecular markers.