Traditional Chinese medicine (TCM) exhibits a broad range of effects on biological activity that is probably due to interactions of complex chemical constituents with multiple targets in the body. Understanding the active chemical constituents in TCM is very important in providing rationales for the clinical usage of TCM. The zebrafish (Danio rerio) has recently become a popular model in the field of drug screening, specifically emerging as an important vertebrate model for in vivo high-content drug screening of multiple efficacy parameters and whole-organism toxicity. The authors also discussed the advantages of the zebrafish model for evaluating drug metabolism. Zebrafish usage in TCM screening should be a viable approach that helps identify active chemical markers, biological pathways and mechanistic actions of TCM.