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The pomegranate fruit is one of the most important horticultural products due to the presence of polyphenolic, antioxidant and anti-fungal compounds. In the present study, morphological and phytochemical compounds diversity was investigated in eight Iranian commercial pomegranate cultivars. Fourteen morphological characters and 10 chemical compounds were measured. Based on PCA analysis the most variable morphological characteristics among Punica cultivars studied were the wood surface, the leaf tip, the leaf incision, growth power and rained condition. High-performance liquid chromatograms of chlorgenic acid, caffeic acid, Para Coumaric acid as well as titrable acidity, total soluble solid, total phenolic contents, antioxidant activity in juice and peel of cultivars differentiated the cultivars studied. Comparing the two UPGMA dendrograms of Punica cultivars based on morphological data and chemical contents indicated certain disagreement between them. The correlation between morphological and chemical compounds and geographical distances of Punica cultivars was not statistically significant by the Mantel test. These findings indicate that Punica cultivars studied differ in their genetic content, however, this genetic difference is not correlated with their geographical distance.