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. 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