Two red pomegranate cultivars ‘Hongbaoshi’ and ‘Moshiliu’ were sampled as plant materials. The transcriptional characterizations of CHS, CHI, F3H, DFR, ANS, and UFGT involved in anthocyanin biosynthesis were monitored by qRTPCR during fruit development. The relationships between contents of total anthocyanins in fruit peels and transcription abundance of these genes were also analyzed. Results showed that: (1) during fruit development, the content of total anthocyanins in ‘Moshiliu’ was much higher than that in ‘Hongbaoshi’ pomegranate. The content of total anthocyanins in ‘Hongbaoshi’ increased gradually with fruit development, while in ‘Moshiliu’, the content of total anthocyanins was high at early stages and then decreased at later periods. (2) In ‘Hongbaoshi’ pomegranate, transcripts of CHS, CHI, F3H, DFR, and UFGT were most abundant at early and late stages in fruit development. The transcription level of ANS in ‘Hongbaoshi’ increased gradually and reached the highest amounts at the late phases. In ‘Moshiliu’ cultivar, the transcription levels of all detected genes except UFGT remained high at early stages, and then showed a declining trend afterwards. The expression level of UFGT gene in ‘Moshiliu’ reached peak at middle stage. (3) The correlation analysis results showed that a significant positive correlation between ANS abundance and anthocyanins content in ‘Hongbaoshi’ cultivar, while ‘Moshiliu’ cultivar, there was strong positive correlation between CHS and ANS levels and anthocyanins content. It might be concluded that the different red coloration between two pomegranate cultivars was due to the differential expression of the anthocyanin biosynthetic genes at initial and final phases. ANS gene played a key role in ‘Hongbaoshi’ coloration, CHS and ANS played important roles in anthocyanin accumulation of ‘Moshiliu’ pomegranate.