Investigating resource partitioning of marine predators is essential for understanding coexistence of sympatric species and the functional role they play in marine ecosystems. Baleen whales are a key component of sub-Antarctic ecosystems, foraging predominantly on zooplankton and small forage fish. During the twentieth century, baleen whales were unsustainably exploited across the Southern Ocean. Within the exclusive economic zone of South Georgia and the South Sandwich Islands (SGSSI EEZ) in the South Atlantic, approximately 98,000 fin whales (Balaenoptera physalus) and 16,000 sei whales (B.borealis) were harvested. Despite both species historically occurring in high numbers and feeding in sub-polar waters, little is known about the mechanisms of coexistence. Here, by measuring stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) in archived baleen plates and analysing historic catch data, we investigate resource partitioning of fin and sei whale during the commercial whaling period. Temporal and spatial occupancy at SGSSI EEZ (inferred from whaling catches that occurred between 1904 and 1976), alongside historic stomach contents (from the literature), and δ13C and δ15N results (observed in this study), suggests that despite using a common prey resource there was limited overlap in isotopic niches between the two species, with sei whales using SGSSI waters later in the season and for a shorter period than fin whales. We hypothesise that the isotopic differences were most likely due to sei whales foraging at lower latitudes prior to arrival at SGSSI. Our data provide novel insight into how two sympatric whale species co-occurring at SGSSI during the commercial whaling period may have partitioned resources and provide a potential ecological baseline to assess changes in resource use in recovering whale populations.