<p>As a newly identified and poorly understood physiological disorder, aril paleness negatively affects the quality of pomegranate. This study aimed to shed more light on pomegranate aril color development in relation to the aril paleness disorder by investigating several biochemical and color-related parameters in three pomegranate varieties with differing aril colors and comparing them with samples affected by aril paleness. Moreover, the expression of four important anthocyanin biosynthesis genes [<i>phenylalanine ammonia-lyase</i> (<i>PAL</i>), <i>chalcone synthase</i> (<i>CHS</i>), <i>leucoanthocyanidin dioxygenase</i> (<i>LDOX</i>) and <i>UPD-glucose-flavonoid 3-D-glucosyl transferase</i> (<i>UFGT</i>)] were screened during the fruit development and in aril paleness affected samples. Our results demonstrated a significant correlation between color-related parameters and respective biosynthesis genes in the arils of pomegranate. The expressions of <i>PAL</i> and <i>CHS</i> were significantly lower in the white and paleness affected arils than two varieties with red arils. During sampling dates, the lowest expression of <i>LDOX</i> was recorded in the white pomegranate variety. However, the paleness-affected arils displayed a substantially lower expression of <i>UFGT</i> gene compared to the healthy samples, that is, either naturally white or red colored arils. In addition, analysis of the type and level of anthocyanins revealed significant differences between white-, red-, and paleness-affected arils. No significant differences were observed between healthy and infected arils in terms of hydrogen peroxide, antioxidant capacity, phenolic and ascorbic acid contents in this study. Our data strongly suggested that the expression level of anthocyanin biosynthesis genes, especially down regulation of <i>UFGT</i>, had a more determining role in aril paleness incident in pomegranate than oxidative stresses.</p>