Anthocyanins in the fruit of the Chinese bayberry (Myrica rubra Sieb. & Zucc.) are a major focus of research. In the current study, we investigated anthocyanin, total flavonoid, and phenolic acid profiles, as well as the expression of genes involved in anthocyanin biosynthesis, during fruit development in eight cultivars of Chinese bayberry. Total flavonoid and phenolic acid levels were relatively higher in green stage fruits, decreased in turning stage fruit, and increased in ripe fruit. Anthocyanin profiling revealed a contrasting pattern; anthocyanin levels were lower during fruit ripening and increased sharply in mature fruit. Expression profiling of anthocyanins showed coordinated expression of multiple anthocyanin biosynthesis genes during the development process. However, different genes played a predominant role at different stages. Flavanone- 3-hydroxylase and flavonoid-3'-hydroxylase played predominant roles in the accumulation of total flavonoids and phenolic acids during the early stage of development, whereas chalcone synthase played a predominant role in the accumulation of anthocyanins during the ripening stage, implying regulation of anthocyanins varies with development stage.