Regional variation in the axial skeleton of pinnipeds (seals and walruses) and its correlation with aquatic locomotory behaviour is examined using vertebral functional profiles. The results demonstrate clear morpho-functional differences in the thoracolumbar region of modern pinnipeds (Phocidae, Otariidae, Odobenus) that can be strongly linked to swimming style. Phocid seals have a rigid thoracic region attached to a highly flexible lumbar region with long muscular lever arms providing the necessary mobility and leverage to perform pelvic oscillations. Conversely, otariid seals have extremely flexible inter-vertebral joints along the length of the column which should enhance manoeuvrability and turning performance. They also have greater muscular leverage in the anterior thoracic region to support pectoral oscillations. Odobenus (walrus) shows vertebral characteristics most similar to phocids, but with some otariid qualities, consistent with an intermediate or mixed form of aquatic locomotion, with pelvic oscillation dominating over pectoral oscillation. Comparison of the vertebral functional profiles in the fossil taxon Allodesmus kernensis with those of modern pinniped clades reveals that this extinct pinniped may also have used a combination of pectoral and pelvic oscillatory movements during swimming, but in a manner opposite to that of Odobenus, with pectoral oscillatory movements dominating. This study raises questions about the evolution and diversification of pinniped locomotory behaviours, but also provides the necessary framework to begin to examine axial mechanics and locomotory stages in other fossil pinnipedimorphs and their relatives in more detail.