In February 2004, the discovery of an incursion of the dengue vector Aedes aegypti into the town of Tennant Creek in the Northern Territory caused concern for the Northern Territory health authorities who proceeded to implement a Commonwealth-funded eradication program. To determine the origin of the incursion, we performed a genetic analysis on Ae. aegypti from several Queensland and overseas localities.A comparison of DNA sequences from the mitochondrial cytochrome oxidase 1 gene indicated that the incursion was probably from Cairns or Camooweal. This genetic marker was also useful in identifying a separate Townsville haplotype population and another population on Thursday Island in the Torres Strait that was genetically divergent to the mainland populations. The possible use of this marker as a surveillance tool for identifying the origins of local and overseas incursions is discussed.