Chagas disease remains a public health concern in Brazil and other Latin American countries, mainly due to the potential domiciliation of native triatomine species. We analyzed the genetic variability of Triatoma pseudomaculata in sylvatic and peridomestic ecotopes throughout three localities in the northeastern state of Bahia, Brazil. We studied polymorphisms generated by random amplified polymorphic DNA (RAPD) and isoenzyme electrophoresis analyses. Based on RAPD analysis, each specimen was assigned to one of three genetic clusters. Although all sylvatic specimens from one locality were grouped into the same cluster, sylvatic and peridomestic specimens from the other two localities were broadly distributed between the remaining two clusters, suggesting that geographic population structuring was not occurring. Furthermore, isoenzyme analysis suggested that distinct populations were in Hardy-Weinberg equilibrium. Low statistical values for Wright’s Fst index also supported the absence of population structuring and suggested the occurrence of panmixia. We conclude that genetic flow occurs between sylvatic and peridomestic T. pseudomaculata populations, probably as a consequence of passive and active dispersion of the insects, associated with deforestation and anthropic transformations.