Context. The east and west coasts of Australia form the breeding grounds for two of the world’s largest and fastest-growing populations of humpback whales (Megaptera novaeangliae). These populations show differences in mean lipid content, fatty acid profiles, and stable isotope values.

Aims. To determine whether these differences result in variation in nutritional health and physiology between populations, we quantified and compared the morphology, body condition and energetic requirements between the two populations.

Methods. We used unmanned aerial vehicles to measure body morphometrics (residual of body volume vs length) of humpback whales from May to November in 2017, 2020 and 2021.

Key results. Morphometric measurements were obtained from 973 humpback whales (119 calves, 249 juveniles, 486 adults, and 119 lactating females). Results showed that the two populations did not differ significantly in their morphology. The average body condition was significantly different for sexually mature reproductive classes, with adults and lactating females on the west coast having a lower body condition, by an average of 7.7 and 11.1 percentage points below the east coast population respectively. All reproductive classes, with the exception of calves followed a similar pattern in body condition loss through the breeding season. Calves on the east coast exhibited a curvilinear relationship with days post-partum, with early and late-migrating calves being in poorer body condition than were those migrating mid-season. In contrast, west coast calves did not significantly change their condition through the breeding season.

Conclusions. The poorer body condition of sexually mature individuals in the west coast population is concerning, given the overall condition loss during a breeding season. This difference could be influenced by variations in sampling time; however, differences in feeding opportunities, climatic regimes and/or environmental variables may influence the ability of one population to acquire similar amounts of energy.

Implications. The difference in body condition between these two humpback whale populations highlighted the need to assess populations individually, so as to develop representative levels that can be used for future conservation monitoring and management.