Juniperus excelsa and J. thurifera are considered to originate from the same ancestor. As a result of occurring in geographically isolated refuges –J. excelsa in SE Europe and SW Asia and J. thurifera in SW Europe and NW Africa – their divergence could have taken place at the end of the Tertiary, with the climate cooling. Juniperus foetidissima occurs in SE Europe and SW Asia in territories shared with J. excelsa and is similar to and sometimes misidentified with it. The occurrence of the latter two species over the same area suggests they should be more similar to each other than to the geographically distant J. thurifera. Four populations of J. excelsa ssp. excelsa, four of J. thurifera and two of Juniperus foetidissima were examined on the basis of features of 10 cones and 10 shoots of 18–36 specimens each. Results of discrimination analysis, Mahalanobis distances and cluster analysis showed great similarity to J. excelsa and J. thurifera, while J. foetidissima was more distant. The results support the hypothesis of a common ancestor of J. excelsa and J. thurifera, but suggest another origin of J. foetidissima. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 483–495.