Bats are an important ecological group within ecosystems. The rabies virus is a Lyssavirus, and haematophagous bats are the principal reservoir; however, the virus has also been detected in non-haematophagous bats. The objective was to determine the rabies virus in non-haematophagous bats in the Colombian Caribbean region. In 2017, a cross-sectional study was carried out with a base-risk sampling in twelve geographic zones of the Colombian Caribbean area that included the main ecosystems of two departments. 286 bats were captured, which were euthanized with a pharmacological treatment following the ethical protocols of animal experimentation. The taxonomic identification was done with dichotomous keys. The necropsy was carried out at the capture site, and brain samples were kept in liquid nitrogen. The extraction of the RNA was carried out from the frozen brains with Trizol™; a fragment of 914 bp of the glycoprotein G of the rabies virus was amplified with RT-PCR. The amplicons were sequenced with the Sanger method. Twenty-three genera of bats were identified, and, in two frugivorous, Artibeus lituratus and Artibeus planirostris, amplicons were obtained and sequenced as the rabies virus. This is the first evidence of natural infection of the rabies virus in frugivorous bats in the Colombian Caribbean area; this result is important for the surveillance and control of rabies.