A conjoint analysis of gut contents and stable C and N isotopes was applied to determine the main food sources and feeding habits of dominant amphipods in an eelgrass bed (Zostera marina) in Gwangyang Bay, Korea. Gut content observations demonstrated that, while Gammaropsis japonicus and Jassa slatteryi are herbivorous, feeding on epiphytes and detritus, Pontogeneia rostrata and Monocorophium acherusicum are omnivorous, feeding on mesozooplankton fragments and detritus. Stable isotope data confirmed that epiphytes, detritus, and mesozooplankton fragments were major food sources for amphipods in the eelgrass bed. Isotopic mixing model calculations clearly showed an interspecific difference in diet composition. A high isotopic dissimilarity between amphipod taxa demonstrated interspecific trophic diversity, reflecting their herbivorous (G. japonicus and J. slatteryi) and omnivorous (P. rostrata and M. acherusicum) feeding habits and confirmed the detrivorous feeding habits of caprellids. Such trophic diversity at interspecific level of the amphipod species indicates that they use different food resources within their microhabitats and play species-specific functional roles as mediators in trophic pathways from producers to higher-level consumers of the eelgrass ecosystem. Finally, our findings suggest that information on the species-specific trophic ecology of amphipods is needed to better understand their potential role in the trophic dynamics and carbon flow of seagrass bed ecosystems.