Mediterranean junipers are of special ecological importance as key components of resource islands in semi-arid mountain ecosystems of the Mediterranean basin. The fragmentation of their habitat, which was primarily natural and driven by climatic drought conditions, is currently being aggravated by anthropogenic pressure. In the framework of this concern, the present work aims to contribute establishing a genomic profile of Juniperus in its western Mediterranean range, with a special emphasis placed on J. thurifera. DNA contents were assessed by flow cytometry in 43 populations of nine taxa within their Mediterranean range (first reports for J. navicularis, J. thurifera subsp. africana and J. thurifera subsp. thurifera). Chromosome numbers were determined by orcein staining in eight taxa (first counts for J. oxycedrus subsp. badia, J. phoenicea subsp. phoenicea, J. phoenicea subsp. turbinata, of 2n = 2x = 22, and for J. thurifera subsp. thurifera, of 2n = 4x = 44). Tetraploid cytotypes have been the only ones found in the 19 populations of J. thurifera studied, this being the first report of a Juniperus species exclusively polyploid. In J. thurifera, C-value does not respond to habitat fragmentation, in the same way that genetic diversity within populations was previously shown to be unaltered, suggesting that this factor has not had, at least to date, a significant impact on populations at genomic and genetic levels. Habitat fragmentation leads to deeply age-biased populations with a male-biased imbalanced sex ratio (lack of females), indicating an urgent need to improve regeneration within the populations of this species.