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This study investigated the occurrence of Cytauxzoon felis and Babesia spp. in free-ranging jaguars (Panthera onca), domestic dogs (Canis lupus familiaris) and domestic cats (Felis catus) from the Cerrado, Amazon and Pantanal biomes of Brazil. Blood samples were collected from 30 jaguars, 129 dogs and 22 cats for detection of the 18S rRNA genes of piroplasmids. All of the jaguars from the Pantanal (n=22) and Cerrado (n=4) and three of four jaguars from the Amazon were positive for C. felis, but no dogs or cats were positive for the agent. All of the jaguars and domestic cats were negative for Babesia spp., while dogs from the Cerrado (7.9%; 5/63) and Amazon (10.6%; 5/47) biomes tested positive for the hemoparasite. Cytauxzoon nucleotide sequences detected were closely related to C. felis; and Babesia nucleotide sequences showed 100% of identity with Babesia vogeli. Although the pathogenicity of Cytauxzoon spp. genotypes that circulate in Brazil is still unknown, free-ranging jaguars probably play an important role in the maintenance of C. felis in nature. In addition, even though there is no evidence of the circulation of Babesia spp. between jaguars and dogs, the presence of this hemoparasite should be monitored in jaguar populations.