Significance Anthraquinones are potent secondary metabolites produced by many fungi and plants used in traditional Chinese and Indian medicine. Many display useful biological properties, including antineoplastic, antiinflammatory, antiinfective, or antiparasitic activities. The chemical structure of anthraquinones is very diverse, with many occurring as homo- and heterodimers. Anthraquinone biosynthetic pathways must be elucidated before novel structurally complex chemicals with new or enhanced biological activity can be engineered. In this study, we identified an enzyme involved in asymmetrical dimerization of nataloe-emodin, which results in increased cytotoxicity toward a range of cancer cell lines. Mastering the substrate specificity of this enzyme (and other similar enzymes) could lead to the dimerization of anthraquinone-related compounds with medicinal activities.