Benthic copepods dominate meiofaunal communities from marine phytodetritus, both in terms of numerical abundance and species diversity. Nevertheless, ecological factors driving copepod co-existence and population dynamics are still largely unknown. Here, we aimed to explore feeding habits of four copepod species commonly found in Mediterranean seagrass detritus accumulations, representing distinct eco-morphotypes (planktonic, phytal, epibenthic and mesopsammic). Joint use of fatty acid and stable isotope trophic markers showed that co-occurring harpacticoid copepods have diversified diets. Contrary to what was expected, microphytobenthos does not serve as their main food source. Instead, we found evidence from both techniques that major food items include heterotrophic biomass, macro-epiphytes and, depending on eco-morphology and season, of seagrass detritus-derived organic matter. Isotopic niches suggested that eco-morphotypes showed resource segregation. This segregation varies temporally, and partial overlap occurs between niches of phytal and epibenthic eco-morphotypes in some seasons. Our results highlight that, contrary to what is often assumed for meiofaunal consumers, considerable trophic diversity exists among copepod assemblages. They also indicate that, through multiple non-exclusive possible mechanisms, copepods could constitute a major link between seagrass detritus and associated biomass and higher trophic levels (namely macroinvertebrates and juvenile fish).