Polyphenol compounds are considered valuable to human health mainly due to their high antioxidant activity. The phenylpropanoid pathway is responsible for the synthesis of a large range of polyphenolics including anthocyanins, flavonols, flavones, flavanones, flavanones and isoflavonoids that occur naturally in plant tissues. Anthocyanins are natural pigments which accumulate especially in fruits and flowers. These pigments play important roles in signalling between plants and microorganisms, plant defense, protection against oxidative stress and radiation damage. Although, anthocyanin biosynthesis genes and their transcriptional regulatory genes are well characterized in many plants, anthocyanin production and its regulation is not to be known in fruit trees such as pomegranate. Punica granatum is a rich source of anthocyanin pigments resulting in vibrant colors and anti-oxidant contents. The present study was conducted to elucidate the relationship between the expression levels of anthocyanin biosynthesis genes and the accumulation of anthocyanins during the colour development phase of the pomegranate fruits. The cDNA fragments of four transcription factors (MYB1, MYB2, bHLH and WD40) as well as eight structural genes in anthocyanin biosynthesis pathway( PAL , CHS , F3H , F3'H , F3'5'H , DFR , ANS and UGFT ) were isolated from pomegranate by RT-PCR with degenerated primers. The expression of these genes was assayed in three pomegranate accessions (Poost Siyah Yazd, Bozi Isfahan and Shirin Saabad Shiraz) which had distinct differentiation in skin colour and pattern of colour accumulation by semi-quantitative RT-PCR. Moreover, the full-length of the PgMYB1 , PgMYB2 , PgWD40 , PgPAL , PgCHS , PgF3H , PgDFR , PgANS and PgUFGT genes were isolated and characterized. The obtained resulted revealed that fruit skin coloration is mainly influenced by the concentration of anthocyanin pigments. In three pomegranate accessions, ANOVA showed that in respect to different skin colours, differences between the content of anthocyanin are highly significant (p=0.001). Meanwhile, the observed differences in skin colour is significantly associated with the expression alteration of the regulatory transcription factors. PgDFR , PgANS and PgUFGT expression exhibited a positive correlation with the presence of anthocyanin and the accumulation of PgMYB , PgWD40 and PgbHLH transcripts. These results suggest that the MYB-bHLH-WD40 transcription factor complex control the anthocyanin biosynthesis via activating the expression of PgDFR , PgANS and PgUFGT genes in pomegranate. Based on computational methods, deduced amino acid sequences of the cDNA showed high homology to the sequences from other plants. Each gene is a member of a multigene family. Interestingly, gene network prediction revealed that anthocyanin pigmentation, as a complex trait is controlled by multiple developmental and environmental factors. For the first time, the current work illustrated a clear relationship between transcriptional patterns of anthocyanin biosynthesis pathways and accumulation of representative anthocyanin in pomegranate during fruit development. In fact, the predicted results highlights a complex regulatory network orchestrate the production of anthocyanin pigment. Additionally, this network is stimulated by various developmental and environmental factors. Therefore, pigmentation production is complicated phenomenon consisting a large number of stimuli-inducible genes. The present work is a successful attempt to provide a useful model of anthocyanin biosynthesis network and predict the important proteins. The essential proteins will serve as a basis for future studies that facilitate development/selection of new pomegranate cultivars with enhanced anthocyanin content. Key words : Anthocyanin biosynthesis, Structural genes, Regulatory factor and Pomegranate