Information on the poorly known but ecologically important cephalopod fauna of Subantarctic islands was collected using fishery bycatches, together with published data from oceanographic cruises and top predators (fishes and seabirds) as biological samplers. Overall, the cephalopod fauna from Kerguelen Islands includes at least 38 different species. Oegopsid squids dominate the assemblage over octopods (31 and 6 taxa, respectively), with one species of sepiolid occurring over the shelf. This rich community includes a large diversity of pelagic squids, four benthopelagic cirrate octopods and two endemic benthic octopodids. The results emphasize the importance of ommastrephids, onychoteuthids, cranchiids and a few other squid species in the nutrition of top consumers in the Southern Ocean. The trophic structure of the community of cephalopods (n = 18 representative species) was subsequently investigated by using the stable isotopic signature of their chitinized beaks. δ13C values demonstrated that cephalopods grew in three different marine ecosystems, with 16 species living and developing in Kerguelen waters and two species migrating from either Antarctica (Slosarczykovia circumantarctica Lipinski, 2001) or the Subtropics (the giant squid Architeuthis dux Steenstrup, 1857). Values of δ15N indicate that species living in Kerguelen slope waters encompass almost three distinct trophic levels with a continuum of two levels between crustacean- and fish-eaters, and a distinct higher trophic level occupied by the colossal squid Mesonychoteuthis hamiltoni Robson, 1925. The stable isotopic signature of beaks therefore revealed new trophic relationships and migration patterns and is a powerful tool to investigate the role of the poorly known cephalopods in the marine environment.