High-performance centrifugal partition chromatography (HPCPC) can be used for the rapid isolation of biologically active metabolites from natural sources. The present study investigates the one-step isolation of diphlorethohydroxycarmalol (DPHC), an algal polyphenol, from the brown seaweed Ishige okamurae by HPCPC and its protective effect against 2,2'-azobis dihydrochloride (AAPH) induced oxidative stress in zebrafish embryos. HPCPC was found to be efficient and effective for the isolation of DPHC from Ishige okamurae under optimized solvent conditions, yielding a high purity product. The present purification method helps overcome compound wasting and possible degradation, which cause a low yield in conventional column separations. Further, zebrafish embryos exposed to AAPH were compared with and without DPHC treatment, two days after fertilization for ROS generation, cell death, lipid peroxidation, survival rate, and heartbeat rates. These evaluations revealed that DPHC treatment significantly enhanced protection against oxidative stress in zebrafish embryos. HPCPC was, therefore, established as an efficient DPHC isolation method and could be used for separating other complex phlorotannins from seaweeds.