Marine organisms produce a variety of carotenoids with unique functional groups such as allene, acetylene, acetyl, and hydroxymethyl. Astaxanthin and fucoxanthin are representative marine carotenoids on which numerous studies have been performed. Due to the characteristic conjugated polyene chain and terminal ring structures, both carotenoids can act as strong antioxidants. Major nutritional effects of astaxanthin, such as cardio-, skin-, and ocular-protective effects, are based on its in vivo antioxidant activity. However, the antioxidant activity of fucoxanthin is not largely involved in its characteristic nutritional activity and anti-obesity and anti-diabetic effects. The major molecular mechanisms of both effects involve modulating the expression of related genes and proteins by fucoxanthin metabolites.