In modern agricultural production, where a small number of commercial cultivars dominate, the collection, evaluation, and preservation of germplasm are important tasks to reduce the erosion of genes and preserve biodiversity. The aim of this study is to characterize the morphological and fruit chemical properties of the pomegranate germplasm grown on the East Adriatic coast, including the commercial cultivars ‘Hicaznar’, ‘Granada’, and ‘Wonderful’, and to highlight the characteristics with the greatest discriminating power. The characterization of the tree, leaf, flower, arils, seed, and juice was carried out using the UPOV descriptor. The colors of the peel, arils, and juice were analyzed according to the CIEL*a*b* method, total soluble solids were measured using refractometers, and total acidity was determined by titration with 0.1 M NaOH. The research results showed significant diversity between the cultivars, which were grouped into several clusters using an unsupervised analysis technique. Factors such as plant vigor, plant growth habit, predominant number of leaves per node on young shoots, crown type, fruit shape, fruit shape in cross-section, peel weight, total aril weight, aril weight, number of arils per fruit, seed length and width, seed yield, total acidity, TSS/TA ratio, and color parameters of the peel, arils, and juice showed high variability, indicating their strong discriminating power in determining the phenotypic diversity of pomegranate.