The cotton bollworm, Helicoverpa armigera, is a quarantine agricultural pest for the American continents. It is thought to have invaded the American continents and led the founding of current H. zea populations in the American continents ~1.5 million years ago. This relatively recent divergence is evident via hybridisation under laboratory conditions. Despite periodic incursions of H. armigera into North America, this pest species is not believed to have successfully established significant populations in the New World. For the first time, we provide molecular evidence via mitochondrial DNA (mtDNA), cytochrome oxidase I (COI) and cytochrome b (Cyt b) partial gene sequences the successful recent incursion of H. armigera into the New World, with populations from the state of Mato Grosso (central-eastern and southern regions) in Brazil, likely to have taken place post 2006. The mtDNA haplotypes detected in the Brazilian H. armigera individuals are common throughout the Old World, thus precluding identification of Old World origins of the founder populations. Combining the two partial mtDNA gene sequences we showed that at least two matrilines were present in Brazil, while the inclusion of three nuclear DNA Exon-Primed Intron-Crossing (EPIC) markers identified a further two possible matrilines. Based upon five genetic markers, the Brazilian H. armigera from Mato Grosso likely originated from at least four maternal lineages.