The African penguin, Spheniscus demersus, the only penguin species that breeds in Africa, is endangered, and several diseases including avian malaria, babesiosis, and aspergillosis are common in some populations. From 2002 to 2010, spirochetes morphologically consistent with Borrelia were observed on thin blood smears from 115 of 8,343 (1.4%) African penguins admitted to rehabilitation centers in the Western Cape and Eastern Cape provinces of South Africa. Prevalence rates were significantly higher among chicks and juveniles compared with adults and for birds sampled during the summer months of October to February compared with winter months. The majority of infected birds were ultimately released, despite lack of antibiotic treatment; however, at least one bird is believed to have died of borreliosis based on characteristic gross and microscopic lesions. Analysis of partial flaB gene sequences indicated this was a relapsing fever Borrelia most similar to a Borrelia sp. detected in soft ticks from a seabird colony in Japan. This represents the fourth report of a relapsing fever Borrelia sp. in an avian species and highlights the need for additional studies of potentially pathogenic organisms infecting the African penguin in South Africa.