During a three-year field study, interspecific and interannual differences in the trophic ecology of littoral fish species were investigated in the rocky intertidal of Helgoland Island (North Sea). We investigated trophic niche partitioning of common coexisting littoral fish species based on a multi tracer approach using stable isotope and fatty acids in order to show differences and similarities in resource use and feeding modes. The results of the dual tracer approach showed clear trophic niche partitioning of the five target fish species, the goldsinny wrasse Ctenolabrus rupestris, the sand goby Pomatoschistus minutus, the painted goby Pomatoschistus pictus, the short-spined sea scorpion Myoxocephalus scorpius and the long-spined sea scorpion Taurulus bubalis. Both stable isotopes and fatty acids showed distinct differences in the trophic ecology of the studied fish species. However, the combined use of the two techniques added an additional resolution on the interannual scale. The sand goby P. minutus showed the largest trophic plasticity with a pronounced variability between years. The present data analysis provides valuable information on trophic niche partitioning of fish species in the littoral zones of Helgoland and on complex benthic food webs in general.