Carotenoids were investigated in two species of clams, Rudiapes philippinarum and Meretrix petechialis. Fucoxanthin 3-esters and fucoxanthinol 3-esters were found to be major components, along with crassostreaxanthin A 3-acetate, crassostreaxanthin A, crassostreaxanthin B 3-acetate, crassostreaxanthin B, halocynthiaxanthin 3'-acetate, halocynthiaxanthin, alloxanthin, diatoxanthin, diadinoxanthin, and heteroxanthin. Fatty acids esterified with fucoxanthin and fucoxanthinol were identified as C24:6, C22:5, C22:6, C20:5, C20:0, C20:1, C18:0, C18:1, C16:0, C16:1, and C14:0 from fast atom bombardment-mass spectrometry (FAB-MS) data. Crassostreaxanthin A 3-acetate and crassostreaxanthin B 3-acetate were first isolated and completely characterized by spectroscopic data. Furthermore, possible metabolic pathways of fucoxanthin in clams were proposed.