Long-distance seasonal migrations are a classic animal migration strategy and humpback whales (Megaptera novaeangliae) annually undertake some of the longest seasonal migrations of any mammal. Commercial whaling exploited their predictable migration and breeding/feeding site fidelity, which included the Australian east coast population (IWC Breeding Stock E1) that were almost extirpated due largely to legal whaling on their migratory route (1952–1962) and illegal whaling on their feeding ground (1959–61). An historical understanding of population demographics and fidelity to migration routes and breeding/feeding grounds is critical to assessing the recovery of exploited whale species, and informs an understanding of social learning of migratory routes and destinations. Here we present multiple lines of evidence, including cultural knowledge of First Nations Australians and observations near European arrival (1802), that demonstrates historical breeding philopatry by the E1 population to the Great Barrier Reef (GBR). Sightings within the GBR near the time of extirpation from commercial whaling (1965/67) provide evidence the whales' maintained their migration and retained ‘cultural memory’ of the breeding ground. We propose species evolutionary adaptations (e.g. song, reproductive aggregations) aided the species in minimising mate-finding Allee effects at low density at this time and speculate a temporal extension of the whales' breeding season at low abundance may have further maximised mate-finding opportunities. We present an analysis of contemporary aerial survey and satellite tracking data that supports consistent use of historical areas in the GBR, with implications on the welfare of whales from increased interactions with marine-based human activities.