Chagas disease is a tropical and systemic disease caused by the Trypanosoma cruzi parasite. This parasite has been divided into six discrete typing units (DTU) due to its high genetic diversity. T. cruziI (TcI) is the most prevalent DTU in Colombia and recently associated with cardiomyopathies. The aim of this study was to unravel the genetic variability between a set of 70 TcI clones of individual cells from different geographic regions and hosts using the cDNA sequences of Cytb and SSU. The results showed two genotypes associated with the transmission cycles of Chagas disease in Colombia and support the previous descriptions using SL-IR. Phylogenetic networks were developed by detecting recombination events within TcI. We also tested the phylogenetic relationships below the TcI clones and the TcIII / TcIV sequences by noting the high ratio of the jungle cycle TcI clones to TcIII / TcIV. We corroborate the high genetic diversity shown by TcI, the plausible recombination within this DTU that supports the previous model of genetic exchange proposed in T. cruzi populations. We conclude by inquiring about the need for new studies to elucidate the genetic structure of TcI in endemic countries of Chagas disease.