The carotenoid content and composition of the gonad and gut of the edible sea urchin Psammechinus miliaris were determined. The dominant carotenoid of the gut wall was fucoxanthinol, indicating the degradation of the main carotenoid found in the Phaeophycean algae. Also present in the gut wall was the carotenoid echinenone, a pigment absent from the diet of wild urchins. Its presence in the gut wall indicates that this is a site for metabolism of dietary, algal, β-carotene. Fucoxanthinol and related products are not found in the gonad and instead this organ was found to selectively accumulate echinenone and β-carotene together with a small number of related compounds. Both echinenone and β-carotene were found in two geometric forms, namely all-trans and 9′-cis or 9-cis respectively. Echinenone is predominantly deposited in the gonad as the 9′-cis form, whilst β-carotene is mainly found in the same form as that seen in the algae that, in part, make up its diet in the wild, i.e., all-trans. This indicates that isomerisation of dietary β-carotene occurs as part of the process of accumulating echinenone in the gonad. The colour and overall appearance of the gonads of this wild and food limited population were generally poor. No correlation between CIE L⁎a⁎b chromameter readings or a visual assessment of gonad colour with carotenoid content as determined by HPLC was observed.