The botanical delimitation of Taxus species and cultivars may be facilitated by characterizing the pigment profiles of their red- and yellow-fleshed arils. Therefore, we determined genuine carotenoid profiles of differently colored arils of seven defined cultivars of Taxus baccata L. and Taxus × media Rehder. In-depth HPLC-DAD-ESI/APCI-MSn analyses revealed the presence of 43 carotenoids. Exceptional retro-carotenoids dominated the profiles of all samples assessed. Rhodoxanthin (E/Z)-isomers were predominant in the red-colored arils, resulting in a rather unusual abundance of carotenoid isomers as expressed by ratios of up to 1.3:2.0:0.9 between (all-E)-, (6Z)-, and (6Z,6'Z)-rhodoxanthin, respectively. By contrast, the uncommon yellow arils of Taxus baccata L. 'Lutea' mainly contained eschscholtzxanthin (E/Z)-isomers and esters. Total carotenoid concentrations ranged from 17.00 to 58.78 μg/g fresh weight across all samples assessed. Highest total rhodoxanthin concentrations of 51.33 ± 0.46 μg/g fresh weight were obtained from the red arils of Taxus × media Rehder 'Hicksii'. Overall, Taxus arils represent a promising source of carotenoids and, in particular, of retro-carotenoids with exceptional molecular structures and extraordinary absorption properties.