The accessory pigment alloxanthin is a well-known taxonomic marker for Cryptophyceae in natural seawater. The use of alloxanthin to estimate in situ zooplankton grazing and selectivity on Cryptophyceae was studied using 2 dominant copepods of the southern North Sea, Temora longicornis and Centropages hamatus. High-performance liquid chromatography (HPLC) analyses of water samples and of freshly caught copepods, starvation experiments, and feeding experiments (shipboard bottle-incubations) were carried out. Although alloxanthin was always detected in copepod extracts, (1) no correlation was found with alloxanthin in seawater, and (2) no significant grazing on Cryptophyceae was observed. Results of our gut-evacuation experiments showed that at least 78% of the initial alloxanthin content of T. longicornis and C. hamatus remained after 90 min, whereas fucoxanthin and chloropigments decreased rapidly with time. Alloxanthin and astaxanthin esters were the only pigments remaining in the body of T. longicornis after several hours’ starvation. It is concluded that most of the detected alloxanthin did not originate from the gut but from the body tissues. Our results suggest that alloxanthin is not suitable as a biomarker for quantitative or qualitative estimates of copepod grazing on Cryptophyceae.