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Pinus heldreichii, Bosnian pine, is a tertiary relict of the Balcan and South Italian flora. The aim of this study was to determine if there are differences in morphological characteristics of the cones and seeds. During the months of September and October, we made a selection of 10 trees out of 19 populations in western part of the Balkan. Fifteen cones were collected from each of the selected trees. From the middle part of each cone 30 seeds and scales were selected. We analyzed the following characteristics: cone width, cone length, seed length with wings, wing length, seed length, seed thickness, scale length, scale width, apophysis length, apophysis width, scale thickness and apophysis thickness. The data were analyzed with descriptive and cluster analysis. The obtained results show low level of variability between the populations, but the results of cluster analysis point at the separation of the Albanian and one among the Kosovo populations (Prelevac).