In the Yucatán Peninsula of Mexico, the main vector of Chagas disease is Triatoma dimidiata. Field studies suggest that natural transmission occurs through transient and seasonal invasion of houses by sylvatic/peridomestic triatomines, rather than through persistent domiciliated bug populations. We investigated the genetic structure of T. dimidiata populations, using morphometry and microsatellite markers, to assess dispersal of individuals in this triatomine species and to understand the dynamics of domestic infestation. We observed low phenotypic and genetic differentiation among populations from different villages, with an FST of only 0.0553, which suggested a weak but significant population structure at this level. Similarly low but significant differences were observed among populations from the same village but different biotopes (sylvatic, peridomestic, and domestic), with FST values ranging from 0.0096 to 0.0455. These data suggested elevated dispersal of bugs between biotopes (Nm = 5–25), which was confirmed by likelihood and Bayesian assignment tests. A proportion of bugs collected within domiciles were significantly assigned to peridomestic and sylvatic areas. This study showed that T. dimidiata has important dispersal capabilities that can explain the seasonal pattern of domicile infestation by peridomestic and sylvatic bugs. Therefore, dispersal should be taken into account in the design of effective vector control strategies.