Managing and monitoring the recovery of cetacean stocks from commercial whaling has been at the core of International Whaling Commission activities during the past three decades. However, distribution patterns and habitat preferences of cetaceans on Antarctic feeding grounds are still insufficiently known. This is mainly due to difficulties in collecting cetacean data in remote and seasonally ice-covered Southern Ocean waters. In recent years, habitat models have become an indispensable tool to investigate the spatial structure and functional ecology of cetacean habitats. This study used opportunistically collected sightings of humpback (Megaptera novaeangliae, N = 93) and Antarctic minke whales (Balaenoptera bonaerensis, N = 139) in combination with a range of both static and dynamic environmental variables to investigate the spatio-temporal habitat preferences of both cetacean species on their Antarctic feeding grounds. A maximum entropy algorithm (Maxent) was used to calculate circumpolar spatial prediction maps of habitat suitability on a daily basis to evaluate how species-specific habitat conditions evolved throughout the spring and summer months from 2005-2011. For both species, habitat conditions showed clear time-dependent, lateral and zonal patterns. Suitable humpback whale habitat occurred predominantly in ice-free areas, extending southwards with the retreating sea ice edge. Highly suitable areas largely matched currently assumed locations of humpback whale feeding grounds. Suitable minke whale habitat was consistently predicted within ice-covered areas, highlighting the need to intensify surveys within the pack ice to improve stock assessments. Suitable habitat conditions for humpback and minke whales were spatially separated throughout the spring and summer months, suggesting that each species occupies a distinct, potentially complementary ecological niche within the Southern Ocean ecosystem. This study demonstrates the robustness and strength of habitat models to efficiently further our understanding of cetacean-habitat structures and subsequently improve conservation and management strategies of Antarctic cetaceans.