Objective: To study the eco-epidemiology of alphaviruses in bats of departments of Córdoba and Sucre, Colombia. Methodology: A prospective descriptive cross-sectional study with a non-probabilistic sampling, in 12 localities of Córdoba and Sucre was carried out. Using mist nets capture of the specimens was carried out. The size of the sample was 286 bats, each specimen captured was taxonomically classified. The bats were immobilized with anesthetic and analgesic treatment according to the ethics committee of the University of Córdoba, morphometric measurements and blood samples were taken, later they were necropsied in the field to obtain a collection of tissues which were preserved in liquid N 2 −190°C. The averages of the climatic conditions of the sampling sites were extracted from the WorldClim database (http://www.worldclim.org/). The open source software QGIS (Quantum GIS Development Team.2015) was used to map and visualize bioclimatic regions of Córdoba. We used descriptive and retrospective information about the equine population and reports of foci of equine encephalitis. Results: In Córdoba and Sucre, 286 bats were captured and 23 species were classified, Artibeus and Phyllostomus discolor were the most frequent captured genus. The geographic ranges of the captured species were variable, some had a wide distribution and others were restricted to some areas. Venezuelan equine encephalitis virus RNA was detected in Artibeus planirostris and Sturnira lilium (2/286 = 0.70%) from Cordoba -Colombia. The univariate descriptive analysis showed no significant association for any of the analyzed variables climatic. Conclusions: Frugivorous bats from the Caribbean area of Colombia may be involved in the Venezuelan equine encephalitis virus enzootic cycle.