As a product of recent revisions of the nectivore bat genus Anoura (Glossophaginae: Anourina), new species have been described, and several taxa have been elevated to the specific level in the so-called Anoura caudifer and A. geoffroyi species complexes in the last four decades. The genus has a wide distribution across regions of high ecological complexity, including geographic features, such as the Andes and the Isthmus of Panamá, previously identified as natural barriers that restrict gene flow in other phyllostomid bat genera. Up to date, no analyses have been conducted to investigate the contribution of biogeographic factors on the genetic divergence of the genus. In this work, we analyze barcoding DNA sequences (cytochrome oxidase subunit I, COI) to test for geographic structure among Central and South American populations of the A. caudifer and A. geoffroyi complexes. Our analyses show geographic structure for populations previously identified as the A. geoffroyi lasiopyga, suggesting an independent evolutionary fate for Central American representatives of the genus. We also highlight the presence of unrecognized diversity within the A. caudifer complex from the Pacific coast of northern Ecuador.