This work was aimed at investigating the anatomy and composition of the essential oils from different organs of two Pimpinella species, P. tragium and P. saxifraga, originating from the central part of the Balkan Peninsula. The results of the analysis of the anatomy of the different organs of P. tragium and P. saxifraga showed that they were very similar in terms of the structure of the roots, stems and petioles. The roots showed a secondary structure and the stems had a primary structure with closed collateral vascular bundles. The petioles were cordatum, ribbed with an adaxial groove, and sparsely covered with short unior bicellular non-glandular trichomes with a pointed top (both species) or with long uniseriate, multicellular, non-glandular trichomes (P. saxifraga). Differences were observed in the anatomy of the leaves and in the indumentum of the fruits. The leaves of P. tragium were isobilateral, while those of P. saxifraga were dorsiventral. The P. tragium fruits were pubescent, covered with numerous, multicellular, uniseriate, straight or curved, gradually acuminate non-glandular trichomes, whereas the fruits of P. saxifraga were glabrous. These differences are of ecological and taxonomic significance. Secretory canals were observed in all the investigated organs of both species. The essential oils, isolated by hydrodistillation from the aerial parts with inflorescences, the roots from the flowering and fruiting period, and the fruits of both species, were analysed by GC-FID/MS. Although P. tragium and P. saxifraga essential oils showed certain differences in qualitative and quantitative patterns, all the oils were characterised by the presence of pseudoisoeugenol type phenylpropanoid epoxy-pseudoisoeugenyl-2-methylbutyrate, as well as by that of trinorsesquiterpenes pregeijerene, geijerene and trinoranastreptene. In addition, azulenes were present in all the root essential oils, whereas in the majority of the oils from the fruits and flowering aerial parts the common compound was the sesquiterpene ?-bisabolene. The occurrence of phenylpropanoids of pseudoisoeugenol type and geijerenes is important from the chemotaxonomic point of view and confirms them as chemical markers of the Pimpinella species analysed so far.