Originally described from Africa, the genus Eccopsis Zeller (Lepidoptera: Tortricidae) currently includes 25 Afrotropical and five Neotropical species. Adult morphological characters suggest that the Afrotropical and Neotropical species might not be congeneric. Here we present the first DNA sequences for Neotropical Eccopsis and use these data in a maximum likelihood (ML) analysis to evaluate the monophyly of the genus, and to examine the utility of DNA barcodes in separating the South American E. galapagana Razowski & Landry, 2008 and E. razowskii Vargas, 2011. Intraspecific and interspecific pairwise distances (K2P) were 0–0.5% and 4.9–5.2%, respectively, and each species was recovered as a distinct, well supported group of sequences (i.e., species) in the ML analysis. An analysis including barcodes of Afrotropical Eccopsis (four species), Afrotropical Paraeccopsis (one species), and Neotropical Eccopsis (two species) failed to recover Eccopsis as monophyletic. Consistent with previous suggestions based on adult morphology, this study highlights the necessity to reassess the congeneric status of Afrotropical and Neotropical species of Eccopsis.