Anthocyanins are a group of secondary metabolite that is responsible for the color in plant and their antioxidant activity has been noticed as a health-promoting material. To identify the genes responsible for anthocyanin-enrichment in the black rice grains, we assessed the expression of transcripts in both black and white rice cultivars using the 135K Oryza sativa microarray and found that the 3,728 genes were associated with the production of anthocyanin pigment. Among them, the 573 conserved orthologous genes were identified using the COGs analyses and were compared with the existing flavonoid-pathway network. Enriched-pathway analysis finally resulted in 53 candidates for anthocyanin biosynthesis. These genes were anchored to the chromosomes of the rice genome to identify their genetic-map positions and were subjected to the phylogenetic construction together with their 31 homologous proteins sequences from A. thaliana, using the maximum-likelihood method. Our candidate genes seem to either play a regulatory role in anthocyanin biosynthesis or be related to anthocyanin metabolism.