The Sabina section is one of the three groups in the Juniperus genus and the most diverse. The variability of Mediterranean junipers from the Sabina section is related to their Tertiary and Pleistocene migrations and long-term isolations. Their contemporary taxonomic and geographic diversity was influenced by important events such as the migration of continents, the disappearance of Tethys, orogenic movements or the Messinian salinity crisis. The results of morphological measurements of seed cones, seeds and branchlets with leaves of 19 populations of Juniperus phoenicea complex, J. excelsa s.s., J. thurifera subsp. thurifera and subs. africana, J. foetidissima and J. sabina var. sabina and var. balkanensis were statistically compiled using univariate statistics and multivariate analysis. The most important characters differentiating the populations within the taxa were the thickness of the branchlet and the cone diameter, while between the taxa the ratio of cone diameter to the width of the seeds and the number of seeds per cone were used for speciation. J. phoenicea complex is distinguished from the other studied taxa by the greatest number of characters. J. foetidissima, J. sabina var. sabina and J. canariensis are characterized by the highest variability of morphological characters, while J. excelsa and J. sabina var. balkanensis – the lowest. The studies confirmed the ancient nature of the J. phoenicea complex in relation to other taxa from the Sabina section, as a result of an earlier detachment from the ancestor, and no loss of variability due to the effects of colonization and isolation in J. canariensis. In addition, the similarity of J. sabina and J. thurifera was demonstrated, which would confirm the descent from a common ancestor and similar migration routes from the center of Europe towards the Iberian Peninsula, as well as further differentiation of J. thurifera into subspecies caused by isolation due to the opening of the Strait of Gibraltar. The distinctiveness of J. foetidissima from all the other analyzed taxa was also confirmed, and some morphological similarity was shown, proving the original character of J. excelsa s.s. and its similarity to the J. phoenicea complex in this respect.