The effects of heating and photo-irradiation on the stability of all-E-isomer-rich and Z-isomer-rich xanthophylls, astaxanthin and its structurally related xanthophylls, adonirubin, and adonixanthin, are investigated. The xanthophylls with high Z-isomer content are prepared from their high-purity all-E-isomers by thermal isomerization and filtering techniques, that is, total Z-isomer ratios of adonirubin, astaxanthin, and adonixanthin are 80.9%, 89.5%, and 72.5%, respectively. The all-E-and Z-isomer-rich xanthophylls dissolved in ethanol are stored at 4, 30, and 50°C in the dark and at 30°C under photo-irradiation using a fluorescent light for 21 days. In the all-E-isomer-rich xanthophylls, as the storage temperature increases, the total Z-isomer ratio becomes higher, whereas in the Z-isomer-rich xanthophylls, the all-E-isomer ratio becomes higher. Photo-irradiation slightly promotes Z-isomerization in (all-E)-xanthophylls, but highly promotes all-E-isomerization in Z-isomer-rich xanthophylls. In addition, photo-irradiation prevents thermal Z-isomerization of (all-E)-xanthophylls. Moreover, it is found that some xanthophyll Z-isomers such as (9Z)-astaxanthin are more stable than that of the other Z-isomers against heating and photo-irradiation. These findings can contribute not only to establishing suitable storage conditions for Z-isomer-rich xanthophylls, but also to developing control techniques for the E/Z-isomer ratio of the xanthophylls. Practical Applications: The fundamental data on the stability of xanthophyll isomers against heating and photo-irradiation and finding stable xanthophyll Z-isomers are very important to develop xanthophyll materials rich in the Z-isomers. Moreover, this study clearly shows that the heat treatment enhances the Z-isomerization of xanthophylls, whereas the photo-irradiation enhances the all-E-isomerization and prevents thermal Z-isomerization of them. This information can be utilized in technology for arbitrarily controlling E/Z-isomerization of xanthophylls.