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Abstract Southern hemisphere blue (Balaenoptera musculus intermedia) and fin (Balaenoptera physalus) whales are the largest predators in the Southern Ocean, with similarities in morphology and distribution. Yet, understanding of their life history and foraging is limited due to current low abundances and limited ecological data. To address these gaps, historic Antarctic blue (n = 5) and fin (n = 5) whale baleen plates, collected in 1947–1948 and recently rediscovered in the Smithsonian National Museum of Natural History, were analyzed for bulk (δ¹³C and δ¹⁵N) stable isotopes. Regular oscillations in isotopic ratios, interpreted as annual cycles, revealed that baleen plates contain approximately 6 years (14.35 ± 1.20 cm year⁻¹) of life history data in blue whales and 4 years (16.52 ± 1.86 cm year⁻¹) in fin whales. Isotopic results suggest that: (1) while in the Southern Ocean, blue and fin whales likely fed at the same trophic level but demonstrated niche differentiation; (2) fin whales appear to have had more regular annual migrations; and (3) fin whales may have migrated to ecologically distinct sub‐Antarctic waters annually while some blue whales may have resided year‐round in the Southern Ocean. These results reveal differences in ecological niche and life history strategies between Antarctic blue and fin whales during a time period when their populations were more abundant than today, and before major human‐driven climatic changes occurred in the Southern Ocean.