Eighteen Trypanosoma cruzi strains isolated from two triatomine species from northwest Paraná state were characterized using three techniques: RAPD (Randomly Amplified Polymorphic DNA) with four primers; analysis of D7 polymorphic region of rDNA 24Sa and RFLP (Restriction Fragment Length Polymorphism) of 5' region of COII mitochondrial gene (cytochrome oxidase subunit II). The phenetic three constructed with RAPD data displayed that of 18 strains 15 are genetically closer and three strains formed another group, indicating a low genetic variability among them. The strains couldn´t be grouped according to the triatomine species from where they were isolated and not even according to their geographic origin. The strains grouped with T. cruzi I reference strain, indicating preferential association with the sylvatic transmission cycle of this parasite in Paraná state. Any strain grouped with Trypanosoma rangeli sample, being this specie absent among the studied strains. The polymorphism analyses of rDNA and COII genes displayed the presence of T. cruzi I and T. cruzi II populations, being that in nine isolates (50%), both populations occurred concomitantly. Of these strains, most of them (6/9) were isolated from Triatoma sordida and only three from Panstrongylus megistus. These results suggest that these triatomine species have different capacity of elimination of T. cruzi populations, mainly if it´s considered the greatest alimentary and behavioral eclecticism of P. megistus with regard to T. sordida. Once T. cruzi II has been more frequently associated to chronic infections in humans, the presence of co-infections in vectors implicates in potential risk of T. cruzi transmission and in the importance of studying better the dynamics of the parasite polyclonal populations in northwest Paraná.