In Brazil, about 99% of malaria cases occur in Brazil’s Legal Amazon. In all other states malaria has been noted but with imported cases. Here we describe an autochthonous case of malaria in Petropolis city, Rio de Janeiro. The clinical symptoms and epidemiological aspects were compatible with malaria and the presence of Plasmodium was confirmed through molecular diagnostic testing performed on a blood sample from a local resident after an ecological hike in the Atlantic Forest on the outskirts of town. After treatment with chloroquine and primaquine, the symptoms ceased. This city was regarded malaria free for many years although it still presents the malaria vectors. Considering that Plasmodium sp. is an important cause of morbidity and mortality worldwide, this clinical case serves as an epidemiological alert.