The differences in rorqual feeding ecology have been linked to the presence of different morphological markers. The Antarctic minke whale (Balaenoptera bonaerensis Burmeister, 1867) and common minke whale (Balaenoptera acutorostrata Lacépède, 1804) are closely related species, but their morphological differences have not been fully investigated. In this study, we compared 21 skull and 11 feeding apparatuses (baleen and mouth-related parts) measurement points between these two species using hundreds of individuals covering a wide range of body lengths in both sexes. Their engulfment capacities were estimated using these measurements. Our results show that Antarctic minke whales have (1) proportionally larger skulls to the body length, (2) more dorsoventrally and laterally curved rostra, (3) proportionally larger feeding apparatuses to the condylobasal length, and (4) significantly larger engulfment capacity than common minke whales. These differences could indicate that Antarctic minke whales have developed a feeding strategy suitable for feeding on krill, which forms large schools. In contrast, common minke whales have adapted to prey on small pelagic fishes that are agile and form small schools.