Ion exchange perfusion chromatography has been introduced for the isolation of hydrophobic membrane protein complexes from thylakoid membranes of spinach chloroplasts. By using this chromatographic technique, previously shown to be useful for the rapid isolation of soluble proteins (Regnier, F. E. (1991) Nature 350, 634-635), we have been able to isolate oxygen evolving photosystem II core complexes and photosystem II reaction center particles. Pure reaction centers could be isolated from photosystem II core complexes after a chromatographic step requiring only 6.5 mm, which is a substantial improvement in comparisons with previous procedures. The entire preparation of photosystem II core complexes and reaction center II particles could be completed in less than 2 h. The use of perfusion chromatography, as a versatile method for the isolation of hydrophobic membrane proteins from photosynthetic membranes, as well as for other biological membranes, will be discussed.