The molecular configuration of the xanthophyll cycle carotenoids, violaxanthin and zeaxanthin, was studied in various isolated photosystem II antenna components in comparison to intact photosystem II membranes using resonance Raman combined with low-temperature absorption spectroscopy. The molecular configurations of zeaxanthin and violaxanthin in thylakoids and isolated photosystem II membranes were found to be the same within an isolated oligomeric LHCII antenna, confirming our recent conclusion that these molecules are not freely located in photosynthetic membranes (Ruban, A. V., Pascal, A. A., Robert, B., and Horton, P. (2001) J. Biol. Chem. 276, 24862-24870). In contrast, xanthophyll cycle carotenoids bound to LHCII trimers had largely lost their in vivo configuration, suggesting their partial dissociation from the binding locus. Violaxanthin and zeaxanthin associated with the minor antenna complexes, CP26 and CP29, were also found to be in a relaxed configuration, similar to that of free pigment. The origin of the characteristic C-H vibrational bands of violaxanthin and zeaxanthin in vivo is discussed by comparison with those of neoxanthin and lutein in oligomeric and trimeric LHCII respectively.