Biotransformations of the sesquiterpene ketone nootkatone (1) from the crude drug Alpiniae Fructus and grapefruit oil, and the sesquiterpene hydrocarbon valencene (2) from Valencia orange oil were carried out with microorganisms such as Aspergillus niger, Botryosphaeria dothidea, and Fusarium culmorum to afford structurally interesting metabolites. Their stereostructures were established by a combination of high-resolution NMR spectral and X-ray crystallographic analysis and chemical reaction. Metabolic pathways of compounds 1 and 2 by A. niger are proposed.