Thapsia L. circumscribes a small genus of herbaceous perennials in the taxonomically difficult family Apiaceae. Thapsia occurs around the Mediterranean, extending from the Atlantic coasts of Portugal and Morocco to Crete and other Greek Islands in the East. Thapsia is commonly known as deadly carrot because of the poisonous effects. The resin from species of Thapsia has been used in traditional medicine and included in European pharmacopoeias, and several species contain biologically important sesquiterpene lactones such as thapsigargin. Accordingly, Thapsia has for decades been subject to chemical investigations searching for new specialized metabolites with potential as drug leads. However, no generally accepted taxonomical concept of over 40 species and synonyms exists. In order to address the phylogeny and circumscription of Thapsia, we present the first molecular phylogenetic hypothesis of Thapsia based on sequences of the nrITS region from 50 accessions of Thapsia and representatives of all currently recognized genera in subtribe Daucinae. Phylogenetic analysis using maximum parsimony and Bayesian inference resulted in a well-resolved topology with strong support for inclusion of all the species studied here from Ammodaucus, Distichoselinum, Elaeoselinum, Guillonea and Margotia in Thapsia in correspondence with previous phylogenetic studies of Apiaceae. Elaeoselinum is not monophyletic. Clades within Thapsia correlate well with previous observations of groupings based on the occurrence of biologically important sesquiterpene lactones like thapsigargin and thapsane and derivatives thereof. The result of the phylogenetic analysis necessitates nomenclatural adjustments. Thus, we propose a broader generic concept for Thapsia L. Here Thapsia asclepium, T. gummifera, and T. tenuifolia are reinstated, new name combinations are made for T. leucotricha, T. scabra, and T. thapsioides, and one new species, Thapsia smittii, is established from T. maxima type II.