Mass-specific bone strength was examined in the forelimb and hindlimb of 64 species of birds to determine if aquaflying birds (which utilize the wings for propulsion underwater) differ in their skeletal strength compared with other avian taxa. Long bone strengths were estimated from cross-sectional measurements. Compared with the expectation from geometric similarity, humeral section modulus in volant birds scales nearly isometrically, while femoral strength scales with significant positive allometry. Penguin mass-specific humeral strength is greatly elevated, but the average humeral strength in species that are propelled by the wings in both air and water do not differ from the values calculated in non-diving taxa. However, amphibious flyers have gracile femora. Comparative analyses using independent contrasts were utilized to examine the impact of phylogenetic signal. The residual measured for the penguin–procellariiform humeral strength contrast was larger in magnitude (residual of 2.14) than at any other node in the phylogeny. The data strongly indicate that the transition from an amphibious flight condition to a fully aquatic condition involves greater changes in mechanical factors than the transition from purely aerial locomotion to amphibious wing use. There remains the possibility that a historical effect, such as ancestral body size, has impacted the mechanical scaling of penguins. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 687–698.