The sesquiterpene germacrene D and two deuterium-labeled isotopomers were analyzed by enantio-multidimensional gas chromatography with tandem mass spectrometry in order to investigate mass spectral fragmentation mechanisms. The deuterated analogues were derived from in vivo feeding experiments with 1-[5,5-D2]deoxy-D-xylulose-5-phosphate using intact plant material of Solidago canadensis and were formed by biosynthesis via the methylerythritol phosphate pathway.