A photoaffinity label, 2-azido-9,10-anthraquinone, binds at the quinone-binding (Qφ) site with high affinity and can substitute for the secondary acceptor, phylloquinone, in photosystem I reaction center of spinach. Phylloquinone-depleted photosystem I particles reconstituted with azido-[3H]anthraquinone were illuminated with UV light and analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis. The large core polypeptides (psaA and/or psaB) were selectively labeled. The labeling was competitively inhibited in the presence of anthraquinone. These results indicate that the Qφ site is located on psaA or psaB polypeptides.