Monophyly of pinnipeds (seals, sea lions, and walruses) is well-established. However, it is difficult to reconcile a monophyletic origin of pinnipeds with the disparate locomotory modes and associated skeletal morphologies observed between the extant families. In this study, the skeletal anatomy of Puijila darwini, a key putative stem pinniped from Canada’s High Arctic, is fully described. A biomechanical analysis, using functional limb indices of extant carnivorans to predict locomotory modes in extinct taxa, confirms the aquatic adaptations of Puijila, and identifies it as a forelimb-dominated swimmer. Phylogenetic analyses of molecular and morphological data in isolation recover Puijila as a stem pinniped, and provide strong support for pinniped monophyly. However, a phylogenetic analysis combining molecular and morphological data together recovers an unconventional topology, suggesting the molecular and morphological data are incongruent. Closer scrutiny of previously-proposed pinniped synapomorphies suggests many features shared between seals, sea lions, and walruses arose in parallel.