The trophic niches of 2 common co-occurring ophiuroids, Ophiocomina nigra and Ophiothrix fragilis (Echinodermata, Ophiuroidea), in 2 contrasting coastal systems of Brittany (France) were investigated. We used a combination of fatty acid biomarkers derived from neutral lipids and stable isotopic compositions to explore the contributions of oceanic versus continental inputs to the ophiuroids' diet. We investigated 2 different systems with an inshore versus offshore comparison. We sampled potential food sources and surveyed organisms every 2 mo for 1 yr. Spatio-temporal variations in stable isotopes and fatty acid profiles of the ophiuroids were generally low compared to interspecific differences. Fatty acid markers showed that both ophiuroids relied on diatom inputs. However, a more δ15N-enriched isotopic composition as well as a more balanced plant-versus animal-derived fatty acid composition in O. nigra suggest that a broader range of food sources are being used by this species irrespective of location or sampling time. The positive correlation between the 18:1n-9/18:1n-7 fatty acid ratio and δ15N values indicates a higher trophic position for O. nigra (suggesting an omnivorous feeding mode), whereas O.fragilis appears to be more herbivorous. Moreover, the low polyunsaturated/saturated fatty acid ratio associated with elevated bacterial fatty acid markers indicates that O. nigra preferentially consumes detritus, while O.fragilis relies more on fresh phytoplankton-derived material. Both stable isotope and fatty acid analyses suggest that terrestrial inputs do not contribute significantly to the diet of these ophiuroids. However, phytodetritus derived from decomposing green macroalgae contributed to the diet of O. nigra in the Bay of Douarnenez.