Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It presents one of the most complex crop genome studied to date, mainly due to the very high level of vertical redundancy (2n = ca 12x = ca 120 = 10 Gb), together with an interspecific origin. Modern cultivars are derived from hybridization, performed by breeders a century ago, between two autopolyploid species, namely S. officinarum (domesticated, 2n=8x=80) and S. spontaneum (wild species, 2n=5x=40 to 16x=128). To investigate genome dynamics in this highly polyploid context, we sequenced and analyzed the structural organization of hom(oe)ologous chromosome segments (bacterial artificial chromosome clones) from a few regions of the R570 sugarcane cultivar. For all regions, almost perfect gene colinearity and high gene structure and sequence conservation were observed. Moreover, the vast majority of the homoeologous genes were predicted, based on their structure, to be functional and showed signs of evolving under purifying selection. Compared to sorghum, the sugarcane haplotypes displayed high gene colinearity. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes. Our data suggest the presence of broad sets of functional hom(oe)ologous alleles in its genome, which could explain its unique efficiency, particularly its high phenotypic plasticity and wide adaptation.