Abstract: Cephalopods are an important component of Southern Ocean food webs, but aspects of their trophic ecology remain unresolved. Here, we used archived squid (order Teuthida) beaks, collected from stomach contents of predators at Macquarie and Kerguelen Islands, to investigate the trophic structure within an assemblage of pelagic squids (Alluroteuthis antarcticus, Filippovia knipovitchi, Gonatus antarcticus, Histioteuthis eltaninae, Martialia hyadesi and Brachioteuthis linkovskyi). We combined bulk nitrogen stable isotopes (?15Nbulk) with compound-specific isotope analysis of amino acids (CSIA-AA) to estimate the trophic position (TP) of species and to assess isotopic relationships with body size at the species, community, and ocean basin levels. We observed significantly higher mean ?15Nbulk values for species at the Kerguelen Islands compared to conspecifics at Macquarie Island. This result was explained by regional variability in ?15N values of phenylalanine (?15NPhe), suggesting that predator species were accessing different isotopic baselines at each region. This may highlight the different foraging strategies of both species. The overlap in species TP estimates from CSIA-AA (TPCSIA) between the 2 communities (Macquarie Island TPCSIA min: 2.3, max: 5.3; Kerguelen Islands TPCSIA min: 2.7, max: 5.3) indicated a similar trophic structure at both locations. We note unrealistically low TPCSIA for some species, which we attribute to uncertainty of trophic discrimination factors. TP estimates suggested that squid encompass 3 trophic levels from mid-trophic levels to higher predators. We did not find strong or consistent relationships between TP and body size at either the species- or community-level. One of the largest squid species, M. hyadesi, occupied the lowest TP in both communities. These new insights into the trophic structure of the Southern Ocean squid community have important implications for the future representation of pelagic squids in ecosystem models.