Species of the Citrus genus are known as rich sources of phenolic compounds. Peels of Citrus tachibana and Citrus unshiu are used in herbal formulations, sometimes in similar ways. In this study, we examined the effects of plant maturity and genetic background on the total phenolic contents and quantities of specific flavonoids in C. tachibana peel. In addition, we compared these values in C. tachibana and C. unshiu peels. The total phenolic contents and the contents of nobiletin, tangeretin, and hesperidin were higher in the extracts of the immature peel than in those of the mature peels of C. tachibana ; moreover, the quantities of these compounds were also influenced by the genetic background of C. tachibana . In the extracts of C. unshiu peel, the contents of total phenolics, nobiletin, and tangeretin were lower than those of C. tachibana peel. However, the hesperidin content was higher in extracts of C. unshiu peel than those of C. tachibana peel. This study evaluated the phenolic and flavonoid contents of C. tachibana and C. unshiu in an effort to provide new insights into herbal medicines for further study and utilization.