The recent announcement by the Department of Energy that the soybean genome will be sequenced opens up a whole new arena for gene discovery in this important crop legume. Recent evidence that most of the gene space in soybean may be limited to about a quarter of the genome suggests that a sequence-based gene discovery process will be productive. Along with most flowering plants, the soybean is known to have polyploidy in its evolutionary past.  The importance of genome duplication in shaping plant evolution cannot be underestimated. However, these duplications may become problematic as a whole genome sequence is being consolidated into mega-contigs and pseudochromosomes. To better understand the organization of the soybean genome and to gauge the potential difficulty in reconstructing a whole genome sequence we identified and sequenced several duplicated regions within the genome. Sequence data from duplicated regions suggests that soybean is a mosaic of structure. We observed examples of extensive conservation of gene order and structure as well as regions showing extensive fractionation. Networks of synteny between soybean, Medicago truncatula, Oryza sativa, and Arabidopsis thaliana can be found and suggests that genome sequence from these plants may help in the consolidation of the soybean genome sequence.