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Maca (Lepidium meyenii), mainly grown in Peru, is a traditional herbal medicine that is mostly used to improve sperm motility and serum hormone levels. Maca phenotypes are represented by purple, black, yellow, white, and mixed colors. Recently, a method for Maca cultivation has been established in Japan. Therefore, we determined the effects of different phenotypes and portions on the antioxidant activities and total polyphenols, anthocyanins, and benzyl-glucosinolate contents in Japanese Maca. Purple Maca skin possessed the highest contents of both total polyphenols, antioxidant activity and anthocyanin content in all Macas. Regarding the benzyl-glucosinolate content, white maca had the highest content and was not correlated with antioxidant activity. In the present study, we revealed that purple Maca skin is recommended for high polyphenol content, antioxidant activity, and anthocyanin content. The results of this study will be useful for selecting phenotypes for the improvement of antioxidant activity or hormone balance.