Pinnipeds, semi-aquatic mammals of the order Carnivora, transitioned to the marine environment approximately 25 Mya. This transition was associated with many unique evolutionary pressures, including those affecting the brain. Here we investigate how a semi-aquatic lifestyle may have altered brain morphology in extant pinnipeds using magnetic resonance imaging (MRI) and gross anatomical observations on three spotted seals (Phoca largha, a Phocid) and three Steller sea lions (Eumetopias jubatus, an Otariid).Based on available data, we compared our observations on the semi-aquatic pinnipeds, to both terrestrial, and obligatory aquatic mammals (cetaceans). Pinniped brains exhibited a more disc-like shape, with smaller olfactory bulbs, and expanded temporal lobes, compared to terrestrial mammals, showing some parallels with cetacean brains. Despite conserving primary cortical sulci patterns similar to terrestrial Carnivora, pinnipeds exhibited enhanced secondary sulci, especially in spotted seals with an elevated gyrification index, though not as pronounced as in cetaceans. Like cetaceans, the pinniped hippocampus and corpus callosum are reduced in size, while the cerebellar and amygdala volumes are comparable to terrestrial species. In addition, Steller sea lions displayed an enlarged pineal gland.These findings highlight distinct neuroanatomical variations in pinnipeds, that suggest aspects of parallel evolution with cetaceans. These parallels may be attributed to the shared physical factors of the marine habitat; however, certain brain regions appear unaffected by this transition. Further research is needed to determine the extent to which brain morphology, evolution, and function, is influenced by the aquatic environment.