Widespread worldwide Peucedanum plants (Apiaceae) have been used for centuries as plant medicines. The polymorphism of this genus is consistent with chemotaxonomically and therapeutically significant differences in the composition of secondary metabolites. GC-MS of Peucedanum tauricum M.B. volatiles from the headspace (HS) and hydrodistilled essential oil (HD), both obtained simultaneously from flowers (FL), immature and ripe fruits (IF, MF) and leaves (L1-L3) collected at the time of harvesting of generative organs, show differences in the chemical profiles of HS and HD from the same parts of the plant, and between organs (FL, IF, MF vs. L1-L3). The presented studies on the variability of biometabolites in the phenological period indicated the optimal harvesting time, focused on two molecular chemotaxonomic markers of PT; guaia-1(10),11-diene and guaia-9,11-diene (in generative organs iHD at 25.5–32.1% and 26.8–33.6%; and in their HS at 29.4–41.3% and 25.0–29.4%, respectively). This is the first report on the analysis of fresh aerial parts of Peucedanum sp. in which GC-MS of HS and HD was performed simultaneously during the vegetation period. The importance, with possible limitations, of GC-MS analysis of HS and HD as an evaluation tool useful in the chemotaxonomy of Peucedanum plants was also discussed.