Background: Rhodnius prolixus is an obligate haematophagous insect and one of the most important vectors of Trypanosoma cruzi, the causative agent of Chagas disease in the Americas. T. cruzi is a highly variable parasite which is not transmitted in the same efficiency by the different triatomine vectors. Because different T. cruzi genotypes are aetiopathologically divergent, further elucidation of the transmission abilities of different Chagas disease vectors is extremely important. Findings: In the present study, the growth behaviour of two T. cruzi isolates, MDID/BR/1993/C45 (TcI) and TBRA/BR/ 1999/JCA3 (TcII), sharing the same microhabitat (intestinal tract) in single and mixed infections, was examined. The distribution patterns and parasite population densities were evaluated at 7, 14 and 21 days after feeding (daf) by quantification of parasites using Neubauer haemocytometric measurements and mini-exon PCR to identify TcI and TcII subpopulations. Parasitic colonization in the small intestine was more successful in the mixed infection model than the single infection models at 21 daf. In the rectal lumen and wall, the growth behaviour of the mixed infection was similar to that of the TcI group, although the total parasite number was lower. In the TcII group, no metacyclic trypomastigote forms were found. PCR analysis of the contents of each dissected region showed different genotype fractions in the mixed infection model, in which TcI seemed to be the predominant isolate. Conclusion: The different growth behaviour of the TcI and TcII isolates in single and mixed infection models demonstrated that possibly an intraspecific factor modulates parasitic development in the intestine of R. prolixus.