A metabolomic database for soybean, developed to target the growing needs of the soybean community. The goal is to provide a one-stop web resource for integrating, mining and visualizing soybean metabolomic data, including identification and expression of various metabolites across different experiments and time courses. It incorporates GC-MS and LC-MS based metabolite-profiling data dynamically linked to metabolite information from other public metabolomic databases, including HMDB and Knapsack. SoyMetDB includes Arabidopsis metabolomic data for cross-species comparisons and can retrieve information including the expression patterns of various experiments for complete or partial metabolite name queries. It also incorporates a pathway viewer tool integrating the data from various experimental conditions and presenting them on the pathways to highlight the expressed metabolite, and identifies the most highly represented pathways for multiple metabolite queries.