Understanding the underlying ecological factors that affect the distribution patterns of organisms is vital for their conservation. Cephalopods such as giant warty squids Moroteuthopsis longimana are important in the diets of marine predators, including grey-headed albatrosses Thalassarche chrysostoma, yet our understanding of their habitat and trophic ecology remains limited. We investigated the habitat and trophic niche utilised by M. longimana through the δ13C and δ15N profiles captured in their beaks. M. longimana beaks were collected around grey-headed albatross nests at the Prince Edward Islands during 2004 and 2013 (n = 40 beaks). The results showed distinctly Antarctic distributions (δ13C = -24.0 ± 1.0‰, mean ± SD) for M. longimana, consistent with albatrosses foraging at the Southwest Indian Ridge, as opposed to broader foraging zones utilised by albatrosses from Îles Crozet and Îles Kerguelen. Slightly lower δ15N values (5.4 ± 0.7‰) were found compared to other islands in the Indian Sector of the Southern Ocean, which may indicate more crustaceans in the squid diets. Sequential sampling along the lateral walls of individual beaks (n = 4) revealed ontogenetic shifts in δ13C and δ15N values, but individual variation in these shifts requires further investigation.