Baleen whales are highly mobile marine predators that are still recovering from unsustainable exploitation between the 18th and 20th centuries. There remain considerable gaps in our understanding of the migration, foraging localities, prey choice and population connectivity of whales in the Southern Hemisphere as they recover, the impact of these populations on marine ecosystems, and how they are likely to respond to the ongoing climate crisis. Historic information on population connectivity, distribution and diet prior to exploitation provides a baseline and idealised endpoint against which to assess present-day whale populations. In this thesis, I taxonomically identified historic whalebone assemblages using biomolecular techniques, conducted stable isotope analysis of bone collagen and baleen, and analysed whaling catch locality data to: (i) provide a baseline on the isotopic niches of baleen whales across the western South Atlantic and eastern South Pacific; (ii) document historic patterns of resource partitioning between whale species; and (iii) identify whether sulfur isotopes can be used to infer site fidelity to feeding grounds. In addition, (iv) I combine DNA metabarcoding, population genetics and stable isotope analysis to compare foraging patterns, genetic diversity, and population structure of present-day and pre-exploited populations of the sei whale, Balaenoptera borealis, in the western South Atlantic. Historic isotopic niches and latitudinal feeding ground ranges suggest whale species partition resources in their western South Atlantic and eastern South Pacific feeding grounds. Fin and humpback whales appear to be ecological generalists relative to Antarctic blue whales and sei whales, thus potentially less vulnerable to ongoing environmental change. Historic and present-day populations of sei whales in the western South Atlantic were similar in terms of diet, genetic diversity, and population structure, with isotopic analyses and distribution inferred from historic catch patterns suggesting these whales may be more ecologically specialised than first thought, and therefore vulnerable to environmental perturbations. These inferences provide an important contribution to inform priority assessments for conservation management.