Pinnipeds (seals, sea lions and walruses) are secondarily marine carnivorans that exhibit a wide range of feeding and reproductive specializations. Extant pinnipeds are split into three families: Phocidae (seals), Otariidae (sea lions) and Odobenidae (walruses). Morphometric analyses were used to examine cranial morphology in otariid and phocid pinnipeds. Phocids are more ecologically and taxonomically diverse than otariids, and this study quantitatively assessed the effects of life history, phylogeny and ecology on cranial morphology in these closely related clades of aquatic carnivorans. Fifty-three to 58 three-dimensional landmarks were gathered from 138 specimens, representing 31 of the 33 extant species of otariids and phocids. Principal components analysis was used to identify major axes of variation, and principal component scores were compared with phylogenetic distances and ecological variables to test for significant correlates of skull morphology. Results showed that phocids exhibit a much greater diversity of adult skull morphology than otariids. Shape differences within adult otariids were dominated by males of only one species, Otaria flavescens. In contrast, several species of phocids deviated markedly from the mean phocid morphology. These atypical morphologies were consistently associated with specializations of either feeding or mating strategies. Ontogenetic shape changes are greater, relative to interspecific differences, in otariids than in phocids, and shape dimorphism was observed in only one otariid and two phocid species. Unexpectedly, neither otariids nor phocids showed strong correlations between phylogenetic relationship and cranial morphology. Both clades show strong correlations between cranial shape and some life history and some environmental variables, but phocids show stronger correlations with life-history variables, perhaps reflecting the broad range of reproductive strategies observed in phocids.