Abstract Tubers of the closely related species Solanum tuberosum (potatoes) and Solanum phureja belong to the staff of life for humans. The coloration of the often very colorful tubers is caused by carotenoids (especially xanthophylls) and anthocyanins. The new S. phureja cultivars Mayan Gold and Mayan Twilight, the new S. tuberosum cultivar Red Laura and the traditional S. tuberosum variety Shetland Black were analyzed for their pigment content. The dominant anthocyanin in the red-skinned cultivars Red Laura and Mayan Twilight was characterized as pelargonidin-3-coumarylrutinoside-5-glucoside by LC-ESI-MS. The blue pigment of the Shetland Black cultivar was petunidin-3-coumaroylrutinoside-5-glucoside. Red Laura contained 10 mg anthocyanins g −1 dry weight and Shetland Black 31 mg anthocyanins g −1 dry weight. The main carotenoids in raw tubers are 9- cis -violaxanthin, lutein and one unidentified carotenoid in all S. tuberosum and S. phureja cultivars. Minor compounds were identified as neoxanthin and neochrome. Additionally, zeaxanthin and one further unidentified carotenoid could be found in Red Laura and Mayan Gold. No differences in the carotenoid composition between peel and parenchyma could be found. Total carotenoid content ranged from 2.57 ± 0.53 μg g −1 dry weight in Shetland Black to 14.77 ± 2.22 μg g −1 dry weight in Red Laura (calculated as β-carotene-equivalents). In heat processed tubers, high amounts of carotenoids either changed from all-trans to 9- cis and 13- cis -isomeric form or was degraded. The total pigment content was decreased by heat processing in all cultivars. 8.23 ± 2.98 μg g −1 dry weight could be found in Mayan Twilight and 1.51 ± 0.31 μg carotenoids g −1 dry weight in Shetland Black.