The generation of nonphotochemical quenching of chlorophyll fluorescence (qN) in the antenna of photosystem II (PSII) is accompanied by the de-epoxidation of violaxanthin to antheraxanthin and zeaxanthin. The function of zeaxanthin in two mechanisms of qN, energy-dependent quenching (qE) and photoinhibitory quenching (qI), was investigated by measuring the de-epoxidation state in the antenna subcomplexes of PSII during the generation and relaxation of qN under varying conditions. Three different antenna subcomplexes were separated by isoelectric focusing: Lhcb1/2/3, Lhcb5/6, and the Lhcb4/PSII core. Under all conditions, the highest de-epoxidation state was detected in Lhcb1/2/3 and Lhcb5/6. The kinetics of de-epoxidation in these complexes were found to be similar to the formation of qE. The Lhcb4/PSII core showed the most pronounced differences in the de-epoxidation state when illumination with low and high light intensities was compared, correlating roughly with the differences in qI. Furthermore, the epoxidation kinetics in the Lhcb4/PSII core showed the most pronounced differences of all subcomplexes when comparing the epoxidation after either moderate or very strong photoinhibitory preillumination. Our data support the suggestion that zeaxanthin formation/epoxidation in Lhcb1-3 and Lhcb5/6 may be related to qE, and in Lhcb4 (and/or PSII core) to qI.