Molecular markers are powerful tools to better understand the complex genetics of sugarcane and to assist breeders in genetic improvement of varieties. Restriction Fragment Length Polymorphism (RFLP) markers reveal an important polymorphism in the genus Saccharum. They are thus very efficient for varietal identification, control of pedigree, and varietal diversity studies. Development of diagnostic markers based on Polymerase Chain Reaction (PCR) technology has been undertaken. These markers are simple and quick to perform and thus more adapted to screening large breeding populations. Such a marker is already routinely used for the rapid identification of true Saccharum x Erianthus hybrids in base broadening programs. In situ hybridization on chromosomes enable the exact determination of genomic composition of interspecific hybrids and is thus useful to monitor chromosomes during introgression programs. Currently, efforts are focused on the identification of molecular markers linked to genes of agronomic interest. Recent results obtained with the identification of a marker linked to a major gene for rust resistance in the variety R570 are promising. This cooperative work between CIRAD and WICSCBS already has helped in confirming the hybrid nature of Officinarum x Erianthus hybrids and the doubtfulness of authenticity of some commercial x Erianthus hybrids.