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Anthocyanin is a class of water-soluble flavonoids found in Chinese bayberry (<i>Morella rubra</i>) that is not only responsible for the variety of colors visible in nature but also has numerous health-promoting benefits in humans. Through comparative transcriptomics, we isolated and identified a transcription factor (TF) of the R2R3-MYB type, MrMYB9, in order to explore the anthocyanin biosynthesis pathway in red and white Chinese bayberries. MrMYB9 transcript was positively correlated with anthocyanin level and anthocyanin biosynthetic gene expression during Chinese bayberry fruit maturation (R-values in the range 0.54–0.84, <i>p</i> < 0.05). Sequence analysis revealed that MrMYB9 shared a similar R2R3 domain with MYB activators of anthocyanin biosynthesis in other plants. MrMYB9 substantially transactivated promoters of anthocyanin biosynthesis-related EBGs (<i>MrCHI</i>, <i>MrF3’H</i>, and <i>MrANS</i>) and LBGs (<i>MrUFGT</i>) upon co-expression of the <i>AtEGL3</i> gene. Our findings indicated that MrMYB9 may positively modulate anthocyanin accumulation in Chinese bayberry.