High-speed counter-current chromatography was successfully applied for the first time to the isolation and purification of the bioactive carotenoid zeaxanthin from the cyanobacterium Microcystis aeruginosa. The crude zeaxanthin was obtained by extraction with organic solvents after the microalgal sample had been saponified. Preparative high-speed counter-current chromatography with a two-phase solvent system composed of n-hexane-ethyl acetate-ethanol-water (8:2:7:3, v/v/v/v) was successfully performed yielding zeaxanthin at 96.2% purity from 150 mg of the crude extract in a one-step separation. The recovery of zeaxanthin was 91.4%. This was also the first report that zeaxanthin was successfully separated and purified from microalgae.