ABSTRACT: The Southern Ocean exhibits substantial spatio-temporal variation in biogeochemical processes that shape interactions and productivity across food webs. Stable isotopes in marine predators provide an opportunity to capture such variations. Yet few studies have accounted for variability in the isotopic baseline when interpreting predator isotope values. Using bulk δ15N and δ13C values and the δ15N values of amino acids (AAs) of blood from female Antarctic fur seals (AFS) Arctocephalus gazella, we investigated spatial and seasonal variation in baseline δ15N (δ15Nbaseline) values across 3 Southern Ocean basins (Indian, Pacific and Atlantic) to facilitate robust comparison of consumer trophic ecology. We detected spatial and seasonal differences in δ15Nbaseline values across the basins, using the source AAs phenylalanine (Phe) and lysine (Lys), consistent with the latitudinal gradient of AFS colonies and seasonal changes in seal foraging movement. The δ15N values of source AAs from Marion Island and Cape Shirreff were representative of particulate organic matter δ15N values in the Indian and southwest Atlantic sector respectively, whereas more complex patterns were observed in the Atlantic sector around Bird Island. Variations in bulk δ15N values can also be attributed to changes in AFS diet, with females foraging in the Atlantic and Pacific targeting higher trophic level prey in winter. Trophic position estimation using Phe and leucine (Leu) suggested that females encompass more than 2 trophic levels. Our study highlights the utility of using Lys alongside Phe to assess seasonal and ocean basin-level variations in the isotopic baseline and Leu/Phe for AFS trophic position estimation.