Traditionally, pomegranate (Punica granatum L.) has been consumed as fresh fruit or as pomegranate juice. In this study, the main phenolic compounds of 12 pomegranate varieties and 5 pomegranate clones were determined by HPLC−DAD−ESI-MS. Two chromatographic methods with a fused-core C18 column and a classical HPLC system were developed. Thirteen anthocyanins and fourteen other phenolic compounds were determined in the pomegranate juices. As far as we are concerned, a new flavonol-glycoside, phellatin or its isomer amurensin, has been tentatively identified for the first time in pomegranate juices. Total phenolic content ranged from 580.8 to 2551.3 mg/L of pomegranate juice. Anthocyanins varied between 20 to 82% of total phenolic content. Flavonoids were 1.6-23.6% of total phenolic compounds, while phenolic acids and ellagitannins were in the range 16.4-65.8%. The five clones reported a phenolic content comparable with that of the other pomegranate samples.