The African penguin (Spheniscus demersus) is an endangered seabird that resides on the temperate southern coast of Africa. Like all penguins it is flightless, instead using its specialized wings for underwater locomotion termed 'aquatic flight'. While musculature and locomotion of the large Antarctic penguins have been well studied, smaller penguins show different biochemical and behavioural adaptations to their habitats. We used histochemical and immunohistochemical methods to characterize fibre type composition of the African penguin primary flight muscles, the pectoralis and supracoracoideus. We hypothesized the pectoralis would contain predominantly fast oxidative-glycolytic (FOG) fibres, with mainly aerobic subtypes. As the supracoracoideus and pectoralis both power thrust, we further hypothesized these muscles would have a similar fibre type complement. Our results supported these hypotheses, also showing an unexpected slow fibre population in the deep parts of pectoralis and supracoracoideus. The latissimus dorsi was also examined as it may contribute to thrust generation during aquatic flight, and in other avian species typically contains definitive fibre types. Unique among birds studied to date, the African penguin anterior latissimus dorsi was found to consist mainly of fast fibres. This study shows the African penguin has specialized flight musculature distinct from other birds, including large Antarctic penguins.