Abstract: Gene flow is responsible for the exchange of genes between populations, which promotes the acquisition of alleles that can influence in biological aspects and resilience of T. dimidiata, one of the most relevant species in the transmission of the Chagas disease in Mexico due to the intradomiciliary infestation that it exhibits in rural dwellings, however, recent studies have registered a higher incidence in urban areas. Studies have been carried out on genetic fluctuation in triatomines using molecular markers such as. microsatellites and mitochondrial sequences, however, studies of this type in Mexico for T. dimidiata are scarce. On the other hand, it is unknown how the genetic variability of populations can influence the presence of kdr mutations that confer resistance to pyrethroid insecticides. In this work, the mitochondrial markers ND4 and CytB were used to analyze the components of genetic variation and fixation index within and between the populations collected in the states of Yucatan, Veracruz, and Oaxaca, in addition to detecting the presence of kdr mutations in the para gene of these populations. The use of such molecular tools made it possible to detect a genetic differentiation between the populations, identifying the various haplogroups present, as well as registering the presence of the kdr L1014F mutation associated with resistance to pyrethroids.