Microbial-stressed germination of black soybeans leads to generation of a group of oxylipins, oxooctadecadienoic acids (KODEs, including 13- Z, E-KODE, 13- E, E-KODE, 9- E, Z-KODE, and 9- E, E-KODE), and their respective glyceryl esters in addition to glyceollins, a known phytoalexins present in wild and fungi-infected soybeans. Four fungi, Aspergillus niger, Aspergillus oryzae, Rhizopus oligosporus, and white rice yeast ( Aspergillus niger wry), were applied to compare their efficiency on inducing these compounds during black soybean germination. Overall, R. oligosporus, the starter culture used in tempeh fermentation, gives the highest amounts of KODEs and glyceollins. The glyceollins and KODEs were isolated by preparative HPLC, and the structures were determined by (1)H NMR, UV-Vis, and MS spectra. On the basis of the unequal distribution of the KODEs isomers, an enzymatic reaction, instead of a nonenzymatic free radical chain reaction, is responsible for their formations. Together with other oxylipins and glyceollins, the KODEs may contribute to the soybean's defensive response to fungal infection via reaction with protein thiol groups and cell membranes. The stress-germinated black soybeans may be used as ingredients for further processing of novel functional food products with unique nutritional and flavor profiles.