Many previous studies have shown a great phylogenetic and biological variability of Trypanosoma cruzi using different molecular and biochemical methods. Populations of T. cruzi were initially clustered into two main lineages called TcI and TcII by the size of the mini-exon PCR product. In the present study, 33 isolates derived from three triatomine taxa, which belong to the Triatoma brasiliensis species complex (Triatoma juazeirensis, Triatoma melanica and Triatoma sherlocki); collected in three distinct areas of Bahia state were characterized by PCR. The isolates were identified by the size of the mini-exon gene, 18S rRNA and 24S𝛼 rRNA amplicons. T. cruzi isolates obtained in sylvatic and intradomiciliar ecotopes, derived from T. juazeirensis and T. melanica, were identified as TcI while the parasites originated from T. sherlocki were characterized as TcI and TcII genotypes, respectively. Those species are present in sylvatic ecotopes but are able to infest intradomiciliar areas. Therefore, it would be important to maintain studies in those localities of Bahia and further investigate the possibilities of Chagas disease transmission. Human disease may occur by any T. cruzi genotype and not only by TcII as it is the case in Amazonia.