Abstract: Naphthoquinones are a kind of important active ingredients in the traditional Chinese medicinal herb "Zicao". In recent years, researches on pharmacology and clinical application of naphthoquinones in Zicao have been gradually deepened and made extensive progress around the world. On the other hand, the plant origins of the herbal materials of Zicao in market are complex and their qualities are quite different, thus more and more studies have been focused on the quantitative determination and quality assessment of the medicinal herb as well as its products by using various naphthoquinones as quality chemical markers. In this paper, we review recent advances in the research on pharmacological actions and multi-components content determination of shikonin/alkannin and its derivatives in Zicao so as to provide a scientific guidance for further research and development of medicinal resource of Zicao, and to establish more comprehensive and systematic method for their quality control and evaluation.