In the subfamily Triatominae, the genus Rhodnius is one of the most studied, not only because of its epidemiological importance, but also because of the difficulty in differentiating its species. Currently, one of the strategies to control Chagas disease, besides other initiatives such as the analysis of donated blood, is focused on fighting the vector. Correctly identifying triatomines is essential for the entomoepidemiological surveillance of Chagas disease. The objective of the present work was to compare the species of the R.prolixus complex using geometric morphometry of hemelytra and heads to evaluate the patterns of intraspecific and interspecific allometry and their taxonomic implications. This method can help in the diagnosis of close species, whose morphological characteristics are insufficient for correct identification. Specimens from five different collections were used, covering the species included in the R.prolixus complex (R.barretti, R.dalessandroi, R.domesticus, R.marabaensis, R.milesi, R.montenegrensis, R.nasutus, R.neglectus, R.neivai, R.prolixus and R.robustus). Morphometric analyses indicated that the hemelytra are not structures with good resolution for separating species and, for this reason, the use of the heads proved to be more adequate for this group (thus allowing differentiation of all species of the R.prolixus complex). The results suggest that R.milesi is a variant of R.neglectus and confirms that R.prolixus and R.robustus are distinct species. Furthermore, we propose the creation of the R.neivai complex comprising R.domesticus and R.neivai.