Bioactivity-guided investigation for the rhizomes of Anemarrhena asphodeloides using the Fms-like tyrosine kinase 3 (FLT3) inhibition assay led to the identification of an active xanthone, mangiferin. Mangiferin was found to inhibit activity of the FLT3 wild type and a mutated form of FLT3 with IC(50) values of 0.7 and 1.2 μM, respectively. Furthermore, this compound was assessed with a small panel of select kinases anaplastic lymphoma kinase (ALK), insulin receptor, and epidermal growth factor receptor) and was also found to be active in ALK assay.