Avian malaria is a mosquito-borne disease caused by Plasmodium spp. Avian plasmodia are recognized conservation-threatening pathogens due to their potential to cause severe epizootics when introduced to bird populations with which they did not co-evolve. Penguins are considered particularly susceptible, as outbreaks in captive populations will often lead to high morbidity and rapid mortality. We used a multidisciplinary approach to investigate an outbreak of avian malaria in 28 Magellanic penguins (Spheniscus magellanicus) at a rehabilitation center during summer 2009 in Florianópolis, Brazil. Hemosporidian infections were identified by microscopic and molecular characterization in 64% (18/28) of the penguins, including Plasmodium (Haemamoeba) tejerai, Plasmodium (Huffia) elongatum, a Plasmodium (Haemamoeba) sp. lineage closely related to Plasmodium cathemerium, and a Haemoproteus (Parahaemoproteus) sp. lineage closely related to Haemoproteus syrnii. P. tejerai played a predominant role in the studied outbreak and was identified in 72% (13/18) of the hemosporidian-infected penguins, and in 89% (8/9) of the penguins that died, suggesting that this is a highly pathogenic parasite for penguins; a detailed description of tissue meronts and lesions is provided. Mixed infections were identified in three penguins, and involved P. elongatum and either P. tejerai or P. (Haemamoeba) sp. that were compatible with P. tejerai but could not be confirmed. In total, 32% (9/28) penguins died over the course of 16 days despite oral treatment with chloroquine followed by sulfadiazine-trimethoprim. Hemosporidian infections were considered likely to have occurred during rehabilitation, probably from mosquitoes infected while feeding on local native birds, whereas penguin-mosquito-penguin transmission may have played a role in later stages of the outbreak. Considering the seasonality of the infection, rehabilitation centers would benefit from narrowing their efforts to prevent avian malaria outbreaks to the penguins that are maintained throughout summer.