Pinnipeds are a group of semi-aquatic animals which live on land, but hunt for food in the water. As such, they constitute an apobaramin, similar to bats, which are the only flying mammals. Differentiating between seals (Phocidae), sea lions, fur seals (Otariidae), and walruses (Odobenidae) is therefore an interesting task for baraminology. A morphology-based baraminology study showed discontinuity between phocids and all other pinnipeds. Hybridization results also show that many different phocid genera are capable of interbreeding. Using a gamut of molecular baraminology tools, the mitochondrial DNA, whole genome sequences and proteomes of several dozen pinniped species were studied. The analysis of mtDNA sequence similarity shows that Phocidae, Otariidae, and Odobenidae form their own distinct groups The whole genome analysis shows discontinuity between Otariidae and Phocidae and also Odobenidae. However, discontinuity between Odobenidae and Phocidae is not so clear. Looking at differences in gene content shows discontinuity between Otariidae and the other two pinniped groups. Discontinuity also exists between Odobenidae and the majority of phocids, except for Leptonychotes weddelli. However, a closer examination of orthology groups unique to L. weddelli, Odobenus rosmarus, and the outlier species, Mustela erminea, show that L. weddelli shows continuity with phocids, whereas O. rosmarus shows discontinuity with this group. Ultimately, the morphological evidence, hybridization data, and the results from the molecular baraminology analyses support three separate pinniped holobaramins at the level of the family. There also appear to be several phocid lineages in the subfamily Monachinae, based on mtDNA analysis, such as Lobodon, Mirounga, and Monachus.