Technical Abstract: With the advent of high throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. A set of highly conserved homoeologous segments would be valuable in the exploration of the retention and evolution of genes within gene families due to the evolutionary pressures of polyploidy events and transposable elements. In this report, we provide an example of twelve surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current soybean genome: a genome triplication before the origin of the rosids (~130-240 Mya), a genome duplication early in the legumes (~59 Mya) and a duplication in the Glycine lineage (~13 Mya). These regions in soybean exhibit a much higher gene retention following polyploidy events than is seen in Arabidopsis after its polyploidy events. We also find that approximately one fourth of the transposable elements (TEs) within the twelve homoeologous segments are contained within genes, and we discuss the possible role TE insertion has on genic evolution. Finally, we hypothesize that the presence of one or several families of housekeeping-like genes may be responsible for the high level of conservation of the twelve homoeologous segments.