The genomic landscape of plants, while slowly being charted, is still composed primarily of unknown territory. Many eukaryotic genomes contain isochore regions, mosaics of homogeneous GC content that abruptly change from one neighboring isochore to the next. We identified the long homogeneous genome regions (LHGRs) in soybeans and characterized the families to which they belong. The LHGR pattern of soybeans is unique in that while the a majority of the genes belong to a single family with a narrow GC-range, the family is not the highest in GC content as seen in vertebrates and invertebrates and instead is at 35% GC. The range of GC content for all LHGRs is 16-59% GC which is a lower but larger range than what is typical of vertebrates. We show that the difference in GC content between the LHGRs is mainly in the noncoding regions and the coding regions of the LHGRs remains at about 44% regardless of the surrounding nucleotide composition. This is the first study in which LHGRs have been identified in soybeans.