Pomegranate ( Punica granatum ) is a unique fruit in the world due to containing different compounds such as flavonoids, alkaloids, sterols, tannins and anthocyanins in peel and seed resulting in high economical, pharmaceutical and nutritional values. One of the most important compounds in this fruit is anthocyanins. These compounds that widely found in higher plants, are produced in different organs in response to variety of developmental stages and environmental conditions. Anthocyanins are a large group of water-soluble pigments in plants and they are responsible for the red, purple and blue colors found in many flowers, fruits and vegetables. Also anthocyanins are the major pigments responsible for the pomegranate fruit skin color. There are two groups of genes involved in anthocyanin biosynthetic pathway. First group are structural genes such as Anthocyanidin synthase ( ANS ), Cinnamate 4-hydroxylase ( C4H ), Leucoanthocyanidin reductase ( LAR ), Chalcone synthase ( CHS ) and Flavanone 3-hydroxylase ( F3H ) which are coding pathway’s enzymes and the second group are transcription factors or regulator genes such as Elongated hypocotyl 5 ( HY5 ) which is a kind of bZIP transcription factor, regulates the function of structural genes. Due to the lack of any report about study of quantitative expression of genes involved in anthocyanin biosynthetic pathway in Iranian pomegranate cultivars, therefore the present research focused on expression analysis of these genes ( ANS , C4H , LAR , CHS , F3H and HY5 ) in fruit skin of three Iranian pomegranate cultivars with different colors in eight developmental stages. The anthocyanin content in skin of these cultivars was also measured and its correlation calculated with corresponding genes expression level. For this purpose, firstly, RNA in the peels of three cultivars were extracted using CTAB-based method and their cDNA synthesized. Appropriate annealing temperature of designed specific primer pairs were determined by gradient PCR and expression of six genes in anthocyanin pathway was evaluated by Real-Time PCR reaction. The results indicated that in red peel cultivar ( Malase Esfahan), the highest expression level of all genes were detected in seventh stage. In white peel cultivar ( Shirine Save h ) , the highest expression level of all genes except LAR and bZIP ( HY5 ) was detected in fifth stage and the LAR and bZIP ( HY5 ) showed maximum expression level in the second stage. In Poust Siyahe Yazd cultivar, seventh developmental stage in C4H and F3H had highest expression level, while LAR and CHS in fifth and third stages showed the maximum level of expression, respectively. ANS in third and fifth stages and HY5 transcription factor in second, fifth and seventh stages (without significant differences) had maximum expression level in this cultivar. Totally the highest expression level of all genes except LAR was detected in seventh developmental stage of red cultivar and LAR was showed maximum expression level in second stage of white cultivar. Totally, the highest level of anthocyanin was related to Poust Siyahe Yazd followed by red and white cultivars. Therefore, we can concluded that color of fruit peels in these cultivars are correlated to their anthocyanin levels. Correlation between the total anthocyanin level and expression of the genes involved in its biosynthesis pathway indicated that there was no possibility of direct correlation between them. Key words: Pomegranate, Anthocyanin, Gene expression, Real-Time PCR .