ABSTRACT A major goal of evolutionary ecology is to understand the interaction between ecological differences and the functional morphology of organisms. Studies of this type are common among flying birds but less so in penguins. Penguins (Spheniscidae) are the most derived extant underwater flying birds using their wings for swimming and beak when foraging. The Humboldt Penguin ( Spheniscus humboldti ) and Magellanic Penguin ( S. magellanicus ) occur along the coast of South America and their morphology was compared in allopatry and sympatry throughout their ranges. Measurements included: mass, tarsus length, four beak/head dimensions, bite force, wing loading, and aspect ratio. A thin‐plate spline/relative warp analysis was also used to detect subtle differences in wing shape. Both species generally overlapped in trait morphology, but Magellanic Penguins showed greater trait diversity. Wing morphology was more homogenous between species than beak morphology indicating a similar mode of locomotion but potential differences in prey procurement. Morphological character displacement in sympatry was only evident in beak length. Local adaptation was common in other traits, and Punta Norte (Argentina) was often distinct in having high variation, notably in beak depth, wing loading, and wing shape (relative warp 1). This may be attributed to the fact that penguins here dive deep and forage farther from their colony; they also have a greater colony size that may contribute to greater intraspecific competition for resources. These results support a potentially optimal wing design for aquatic movement, which likely applies to other penguin species. Differences in morphology may also be related to differences between Atlantic and Pacific ecosystems.