It has been shown that the aba mutant of Arabidopsis thaliana (L.) Heynh. is impaired in epoxy-carotenoid biosynthesis and accumulates the epoxy-carotenoid precursor, zeaxanthin (C.D. Rock, J.A.D. Zeevaart  Proc Natl Acad Sci USA 88: 7496-7499). In addition to providing conclusive evidence for the indirect pathway of abscisic acid biosynthesis from epoxy-carotenoids, the aba mutation offers a powerful means to study the function of xanthophylls (oxygenated carotenoids) in photosynthesis. We measured in vivo the chlorophyll (Chl) fluorescence parameters Fo (initial), Fm (maximum), Fv (variable = Fm - Fo), and t1/2 (half-rise time of fluorescence induction) of wild-type (WT) and three allelic aba mutants. The mutant genotypes had significantly lower Fo and Fm values relative to those of WT. The Fv/Fm ratio and t1/2 which are parameters affected by photochemical efficiency, photosystem II (PSII), and plastoquinone pool sizes, were similar in the aba alleles and WT. Because the aba genotypes accumulate high levels of zeaxanthin, which is involved in nonphotochemical quenching of Chl fluorescence, we propose that the reduced fluorescence yields in the aba genotypes are a consequence of the accumulated zeaxanthin. Measurement of PSII oxygen evolution rates in isolated thylakoid membranes of WT and aba-4 confirmed that quantum efficiency was not altered in aba-4 but indicated that the mutant had reduced PSII activity in vitro. Electron microscopy revealed an abnormal chloroplast ultrastructure in the aba plants: the mutants had significantly fewer thylakoid lamellae per granum stack but significantly more grana per chloroplast, as well as more chloroplasts per cell than WT. Immunoblot analysis established that aba-4 had normal levels of the Chl a/b-binding core polypeptide of PSII (CP29) and the PSII light-harvesting Chl a/b-bindtng complex. These results provide evidence for the role of zeaxanthin in nonphotochemical fluorescence quenching and suggest involvement of epoxy-carot-enoids and/or zeaxanthin in thylakoid stacking and PSII activity.