The cotton bollworm, Helicoverpa armigera (Hübner), was recently introduced in Brazil. During the 2012-2013 harvest, producers reported reduced yields up to 35% on major crops. The economic losses reached US$ 1 billion only in western Bahia, triggering a phytosanitary crisis. The deficiencies in existing taxonomic keys to deal with the morphologically indistinct larvae of H. armigera and the native Helicoverpa zea (Boddie) constrained the detection of new incursions of this heliothine invader. This study explored the identity of heliothine larvae that were found infesting soybean- and corn-growing areas from Roraima state, northern Brazil, through sequences of the mitochondrial cytochrome c oxidase subunit I gene. The inter- and intraspecies sequence variations of DNA barcodes in H. armigera and H. zea were analyzed. The genetic diversity and population structure of the specimens from Roraima and two populations from Piauí and Bahia states, northeastern Brazil, were assessed by adding the cytochrome c oxidase subunit II gene to the analysis. Owing to the lack of studies on genetic introgression for the two species, the suitability of using three different nuclear genes to distinguish the two species was also investigated. The results showed strong evidence that the heliothine larvae from north and northeast of Brazil are conspecific with H. armigera, suggesting that this invasive moth has already crossed the Amazon basin. Surveys in the north of South America should start as soon as possible to monitor the entry or spread of this moth in the Caribbean, Central America, and the United States.