Pomegranate is an important source of bioactive compounds that has been used for usual consumption as well as folk medicine for many centuries. This fruit contains high amount of phenolic compounds with health benefits such as antioxidant, anticancer, antiatherosclerotic and neutraceutical properties. Anthocyanins, a subgroup of flavonoids of phenolic are known to be responsible for the pomegranate peel and flesh color. In the present study total phenolic contents (TPC) and anthocyanin profiles of red-, black- and white-peel pomegranates of 23 varieties obtained from Isfahan and Yazd provinces were characterized. The TPC of peels and seeds were extracted using Soxhlet extractor with MeOH and determined according to the Folin-Ciocalteu procedure (TAE). Data were analyzed statistically using analysis of variance and differences among the means were determined for significance at P 0.01 using Least significance difference (LSD) test and the system programmer SAS.v.8. TPC of peel and seed ranged 37 to 176.1 and 0.84 to 2.5 mg/g of dry material respectively, and in juice 0.95 to 3.78 mg/ml. Highest TPC in juice, peel and seed extracts were found in cultivars Sefide-e-Ilam (white peel), Piyazi-Ghasr-e-Shirin (red) and Shirin-e-Pust Siyah-e-Yazd (black) cultivars respectively. It was concluded that there were no clear relationship between skin color and phenolic contents in cultivars that we analyzed. Nevertheless, results indicated that peel extract possessed high amount of phenolic, compared to seed (64 times more). Anthocyanins of the skin were also extracted and analyzed by Thin layer chromatography (TLC) followed by High performance liquid chromatography (HPLC) equipped with DAD and mass spectrometry. For TLC a solvent system comprising of butanol: acid formic: water: hexan (40:15:40:5) were selected amongst 21 other combinations for its resolving power for anthocyanins. Using this system, no anthocyanins were detected in white pomegranate although peels of red and black pomegranate were found to contain abundance of various cyanidin and pelargonidin derivatives. In addition, we identified a delphinidin in black pomegranate peels. To our knowledge this is the first report of this compound in pomegranate peel.