Molecular diversity was analysed among 160 sugarcane clones consisting of 109 modern cultivars mainly from Barbados and Mauritius and 51 of S. officinarum species, which is the major source of genes in modern cultivars. Twelve low copy nuclear RFLP probes scattered over the genome were applied. Although only a few clones of S. officinarum were used in the genealogy of sugarcane cultivars, they encompassed most of the diversity observed within this species. Moreover, more than 80% of the markers present in the whole S. officinarum sample were also present in cultivars due probably to high heterozygosity and polyploidy. A distinct separation was observed between the two main groups of cultivars, Barbados and Mauritius. This appeared essentially due to S. spontaneum alleles present in Mauritian cultivars and absent in Barbadan ones. Linkage disequilibrium was also investigated in a population of 59 cultivars using 38 RFLP probes regularly distributed over the sugarcane genome map. Associations were observed between 33 loci separated by less than 10 cM. This disequilibrium is interpreted as the result of the foundation bottleneck related to the history of sugarcane cultivars. A practical application is that markers can be used to track known QTL in modern breeding materials without the necessity to repeatedly study segregating progenies.