Technical Abstract: The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross-species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 LTR-retrotransposon (LTR-RT) families that are comprised of 32,370 elements in soybean. Approximately 87% of these elements were located in recombination-suppressed pericentromeric regions, where the ratio (1.26) of solo LTRs to intact elements (S/I) is significantly lower than that (1.62) of chromosome arms. Further analysis revealed a significant positive association between S/I and LTR sizes, indicating that larger LTRs facilitate solo LTR formation. Phylogenetic analysis revealed 7 Copia-like and 5 Gypsy-like evolutionary lineages that had existed before the divergence of dicot (e.g., Arabidopsis) and monocot species (e.g., rice), but the scales and timeframes within which they proliferated vary dramatically across families, lineages and species, and notably, one of the 7 Copia-like lineage has been lost in soybean. Analysis of physical association of LTR-RTs with centromere satellite repeats identified two putative centromere retrotransposon families of soybean (CRS), which were grouped into the CR (e.g., CRR and CRM) lineage of grasses, indicating that the functional specification of CR predate the bifurcation of dicots and monocots. However, a number of families of the CR lineage are not physically associated with centromeres, suggesting that their CR roles may have been defunct. Our data also suggest that the putative Copia retrovirus-like family, SIRE, is likely derived from the Gypsy retrovirus-like Athila lineage, and thus we propose a hypothesis of the single ancient origin of retrovirus-like elements in flowering plants.