Carotenoids have received much attention from biologists because of their ecological and evolutionary implications in vertebrate biology. We sampled Galápagos land iguanas (Conolophus subcristatus) to investigate the types and levels of blood carotenoids and the possible factors affecting inter-population variation. Blood samples were collected from populations from three islands within the species natural range (Santa Cruz, Isabela, and Fernandina) and one translocated population (Venecia). Lutein and zeaxanthin were the predominant carotenoids found in the serum. In addition, two metabolically modified carotenoids (anhydrolutein and 3'-dehydrolutein) were also identified. Differences in the carotenoid types were not related to sex or locality. Instead, carotenoid concentration varied across the localities, it was higher in females, and it was positively correlated to an index of body condition. Our results suggest a possible sex-related physiological role of xanthophylls in land iguanas. The variation in the overall carotenoid concentration between populations seems to be related to the differences in local abundance and type of food within and between islands.