The article describes the epidemiology, macroscopic and histological lesions as well as the isolation of Aspergillus flavus and A. fumigatus from Magellanic penguins (Spheniscus magellanicus) during recovery in the Center for Recovery of Marine Animals (CRAM -32ºS/52ºW), over a period of two years. From January 2004 to December 2005 the Center received 52 Magellanic penguins, and 23% (12/52) died. Necropsies were performed and tissue samples were collected for histological and microbiological examination. From 12 dead animals, aspergillosis was confirmed in five animals, corresponding to 42% of the mortality. Granulomatous nodules were observed mainly on air sacs and lungs. Histologically, septate and branching hyphae, measuring 3-5 µm and PAS positive were found. Two of these cases were caused by A. fumigatus, two other by A. flavus, and in one the diagnostic was established by macroscopic lesions observed in the necropsy without sample collection for fungal isolation and identification. The five aspergillosis cases occurred in the first year of the study, when a disinfection program was not yet established in the CRAM. This paper points out the importance of aspergillosis in the rehabilitation process of captive penguins, and emphasize the necessity of an environmental disinfection on the aspergillosis prevention, mycosis that caused a high rate of mortality of the seabirds found on the Brazilian coast and admitted in the CRAM.