We report a series of invasive pulmonary aspergillosis in green turtles (Chelonia mydas) on the southern coast of Brazil. During 13 months period, seven animals were recovered on the coastal beach and sent to a rehabilitation center, dying after a period of captivity up to 27 days. Granulomatous nodules in the lung, with the presence of hyaline and septate hyphae were found in all. Invasive aspergillosis was confirmed by real-time PCR. Our study is the first to describe Aspergillus sp. infection in green turtles. Prospective studies are necessary to evaluate the impact of such severe fungal diseases in sea turtles.