Anthocyanins are a major class of flavonoids that are produced in the tissues of many plant species in response to environmental signals. The pigmentation of Chinese cabbage ( Brassica rapa ) was analyzed using newly developed 300K Brassica rapa microarrays. The significantly expressed genes were analyzed by clusters of orthologous groups (COGs) and hypergeometric analyses for transcription factors associated with anthocyanin pigmentation. The candidate genes were classified into 11 groups that exhibited functionally diverse transcription factor activity involved in anthocyanin-based pigmentation. Thirty-eight unknown genes were identified that potentially play a role in anthocyanin biosynthesis. Three of these unknown genes differed dramatically among cabbage leaves with yellow, green, or red pigmentation. These three genes may play a regulatory role in the anthocyanin production process or may be related to anthocyanin metabolism during flavonoid biosynthesis. These results show functional diversity of transcription factor families and that the biological functions of the anthocyanin-related transcription factors may be activated in a pigmentation signaling pathway in Chinese cabbage ( Brassica rapa ).