The vertebral column has a very important role in locomotion in aquatic mammals, such as pinnipeds. However, the mode of aquatic locomotion differs between pinniped groups. Otariids generate thrust with their forelimbs (pectoral rowing) while phocids move laterally the pelvic region (pelvic oscillation). Therefore, to explore differences between these groups can provide new clues about the evolution of the land-to-sea transition in pinnipeds. In this study, we explore the disparity and morphological integration of the presacral vertebrae of a set of living and extinct pinnipeds. The results obtained show that vertebral morphological disparity is higher in phocids than in otariids. In addition, disparity through time analyses indicate that, for most vertebrae, otariids subclades tend to explore different regions of the morphospace, whereas phocid lineages overlap within similar regions. Finally, the study of integration between vertebrae in otariids reveals an absence of a modular pattern along the spine, in contrast to the modular pattern found in phocids. These results suggest that adaptation to the aquatic environment in both groups follows two completely different pathways, probably associated with their mode of aquatic locomotion. Future studies on the biomechanics of the pinniped vertebral column may confirm the association of morphology and evolutionary patterns with locomotor performance.