The progress that has been achieved in understanding sugarcane (Saccharum spp.) genome structure over the last 15 years, thanks to the development of molecular cytogenetics is reviewed here. The basic chromosome numbers of the species S. spontaneum, S. officinarum and S. robustum have been determined using fluorescent in situ hybridization (FISH) with rDNA probes. Genomic in situ hybridization allowed the differentiation of chromosomes from S. officinarum and S. spontaneum, the two species involved in the origin of modern sugarcane cultivars, assessment of the proportion of chromosomes of these species in the genome of the modem cultivars and assessment of the extent of interspecific chromosome recombination. GISH has also been used to clarify the origin of the related taxa S. barberi and S. sinense. These techniques also proved to be very useful in monitoring introgression from the related genera.