Sugarcane (Saccharum spp.) has been recognized as one of the world's most efficient crops in converting solar energy into chemical energy and having the most favorable input/output ratio. Beside its importance for sugar production it is thus also a primary energy crop. Sugarcane also presents one the most complex crop genomes studied to date. Modern sugarcane cultivars derive from the combination of two polyploid species: S. officinarum, the domesticated sugar-producing species with x=10 and 2n=8x=80, and S. spontaneum, a vigorous wild species with x=8 and 2n=5x=40 to 16x=128 and many aneuploid forms. Both species are thought to have an autopolyploid origin. Modern sugarcanes are highly polyploid (more than decaploid) and aneuploid, with around 120 chromosomes and a genome size of around 10 Gb. They typically display 70 to 80% of chromosomes entirely derived from S. officinarum, 10 to 20% from S. spontaneum and a few chromosomes derived from interspecific recombination. Their meiosis mainly involves bivalent pairing and chromosome assortment results from a combination of polysomy and preferential pairing. We investigated genome dynamics in this highly polyploid context by analyzing the sequence of hom(oe)ologous haplotypes (BAC clones) from the sugarcane cultivar R570. We first analyzed two homoeologous haplotypes from a gene-rich region bearing the Adh1 gene (Jannoo et al 2007), knowing that this region has been thoroughly studied within the Poaceae family. We then analyzed seven hom(oe)ologous haplotypes from a second gene-rich region. Our results indicated that the two Saccharum species diverged 1.5-2 mya from one another and 8-9 mya from sorghum. The sugarcane hom(oe)ologous haplotypes showed a very high colinearity as well as very high gene structure and sequence conservation. A high homology was also observed along the non-transcribed regions to the exception of transposable elements (TEs). Conversely, TEs that represent in average 33% of the BAC clones studie