Heart transplantation is an effective treatment for Chagas disease patients with severe cardiomyopathy. However, Trypanosoma cruzi reactivation is of great concern. The T. cruzi parasite is classified into six discrete typing units (DTUs identified as TcI-TcVI). It is unknown whether there is an association between T. cruzi genetic lineages and the different clinical manifestations of the disease. We report the case of a 51-year-old man who received a heart transplantation and presented with a reactivation of the disease. The molecular characterization of the parasite showed that the reactivation was related to specific infection by a DTU I (TcISYL) parasite.