Abstract: We report the trophic structure of a myctophid assemblage by measuring the isotopic niches of 14 species living in Kerguelen waters, southern Indian Ocean. Most of the species show distinct isotopic niches that differ by at least one of the two niche axes (d13C habitat and d15N trophic position), indicating trophic partitioning within the assemblage. Strong niche segregation occurs within each of the three most common genera of myctophids (Electrona, Gymnoscopelus, and Protomyctophum), illustrating the different mechanisms (habitat and dietary segregation) that allow coexistence of closely related species. Calculated trophic levels (TLs) of myctophids ranged from 3.3 to 4.2, showing that they are secondary and tertiary consumers in the pelagic ecosystem. The positive relationship between TL and standard length of fish points out a structuring effect of size, with larger species (Gymnoscopelus spp.) occupying a higher trophic position than smaller species (Krefftichthys anderssoni and Protomyctophum spp.). Myctophids occupy an intermediate trophic position between macrozooplanktonic crustaceans and seabirds and marine mammals within the pelagic ecosystem. However, the TLs of large myctophids overlap those of crustacean-eating seabirds e.g., Eudyptes spp. (crested penguins) and Pachyptila belcheri. The isotopic niche of myctophids indicates that Aptenodytes patagonicus (king penguin) adults prey upon K. anderssoni when they feed for themselves, thus exemplifying the usefulness of isotopic datasets on potential prey of predators to depict trophic relationships.