Triatomines, or kissing bugs, are vectors of Chagas disease to humans. This disease is a substantial public health problem affecting up to 12 million people throughout the Americas, and its control relies mainly on the insecticide treatment of triatomine-infested houses within villages. In this article, Fernando Monteiro, Ananias Escalante and Ben Beard review how molecular markers have been used to clarify triatomine systematics, and give examples of how our understanding of triatomine population structure and accurate vector identification can be used to optimize vector control.