In Europe, Juniperus sabina L. is a mountainous, rare species that creates small, scattered populations, suggesting their refugial nature. Recently, a new variety of this juniper, J. sabina var. balkanensis R. P. Adams et A. N. Tashev was described based on genetic studies. We expected morphological differentiation among isolated parts of the species range and between varieties, as was the case with other Mediterranean junipers. Cones, seeds and fragments of shoots from a total of 506 individuals were collected from 24 populations in Europe and for comparisons from three populations from Tian Shan. Almost all of the 16 analysed features significantly differentiated among populations and geographical regions as well as between the varieties, although most groups differed from others only in terms of a single feature. The thickness of cones, the width of shoots and the length of seeds were the most important features for differentiation. The geographical structure of the variation of J. sabina was weak, and comparative populations from Tian Shan were clustered with European populations, similar to the findings of a previous study on essential oils. We found slightly different patterns of variation of the two varieties of the species. The little intra-species differentiation could be the result of the long period of contact between nowadays distinct populations and their relatively late separation in the early Holocene.