© 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.Generally, Gundelia tournefortii is considered as the sole representative of the genus and the other species of Gundelia as synonyms. Recent studies suggest that the genus is rich with 22 species. Off these, thirteen are endemic to Turkey. To date, no comprehensive molecular study dealing with speciation exists in the genus. To address the speciation at the molecular level, fresh leaves from 57 samples representing 15 species from their natural ranges in Turkey were obtained by sampling over several years and studied with respect to nrDNA (ITS) and the cpDNA (ndhF) gene regions. Molecular data from cpDNA and nrDNA revealed that there were two major clades. One of these clades consists of G. anatolica, G. glabra and G. asperrima when the ndhF data were used (or just G. anatolica based on ITS data) while the other major clade included the remaining species with subclades. Divergence time and geographical phylogenetic reconstruction analysis indicated that there may be 3 major ancestral associations existing in the studied Gundelia species. Based on ndhF data, the oldest ancestral group included G. anatolica, G. glabra and G. asperrima with the divergence time about 21.27 MYA, while G. tournefortii var. tenuisecta and G. dersim were the most recently diverged group (about 4.66 MYA). Ancestral history of diversity analysis suggested that the dispersal and vicariance events involved in the speciation in the genus Gundelia with complex events of natural hybridization, introgression, geographical isolations or some other weak isolation mechanisms.