Technical Abstract: The SoyTEdb provides resources and information related to transposable elements (TEs) in the soybean genome. The recent availability of the draft sequence of the soybean (Glycine max (L) Merr.) genome has allowed us to identify numerous TEs in this economically important legume crop. Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized. The majority of these TEs (particular a few hundred low-copy number TE families) have not been previously described. These TE sequences have been anchored in and intergrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of TEs from soybean and other related legume species. All TEs or subsets of TEs can be downloaded from the database website http://www.soytedb.org. SoyTEdb represents the most comprehensive and the largest manually curated TE database for any individual plant genome completely sequenced to date, and will facilitate the studies of genome evolution, gene-TE interaction, and epigenomics in legumes and other plant species.