Chagas disease is an enzootic disease, in which the flagellate Trypanosoma cruzi infects a large variety of animals. Humans are accidentally infected due to the migration into wild environments. To identify T. cruzi discrete typing units (DTUs), 19 Brazilian isolates from different biomes and hosts were analyzed by PCR amplification of 24Sα rRNA, 18S rRNA and mini-exon gene sequences. The majority of the isolates was classified as TcIIb (TcII) but subtypes TcIIc (TcIII) and TcIId (TcV) were also identified. In addition, in monkeys TcI was detected.