Regular sampling of wild Paracentrotus lividus was carried out over a 12-month period to examine seasonal effects on the pigment profile and content of the gonads, especially in comparison to gonad colour. The major pigments detected in the gut wall were breakdown products of fucoxanthin, namely fucoxanthinol and amarouciaxanthin A. Lower levels of other dietary carotenoids (lutein and β-carotene) together with some carotenoids not found in the diet, namely isozeaxanthin and echinenone (not, vert, similar 20% total carotenoid) were also detected in the gut wall. The presence of echinenone in the gut wall demonstrates that this organ acts as a major site of carotenoid metabolism. Echinenone is the dominant carotenoid in the gonads, accounting for approx. 50–60% of the total pigment. Both all-trans and 9′-cis forms of echinenone were detected in both the gut wall and in the gonad, with levels of the 9′-cis form typically 10-fold greater than the all-trans form in the gonad. The detection of large levels of 9′-cis-echinenone in wild sea urchins is unexpected due to the absence of 9- or 9′-cis forms of carotenoids in the natural, algal, diet. Whilst echinenone clearly contributes towards gonad pigmentation, levels of this carotenoid, cannot be directly linked to a qualitative assessment of gonad colour in terms of market acceptability. Indeed, unacceptable gonad colouration can be seen with both very low and high levels of echinenone and total carotenoid. The presence of 9′-cis-echinenone as the major carotenoid contributing to the pigmentation/colour of the gonad is an important observation in terms of developing artificial diets for urchin cultivation