Objective. To search Hantavirus and Arenavirus in small rodents and establish their spatial distribution in disturbed ecosystems in the municipality of Villavicencio, Meta, Colombia. Materials and method. A descriptive cross-sectional study was carried out from October 2018 to October 2019 in periurban and rural areas of the municipality of Villavicencio. Rodents were captured using Sherman-type traps and molecular detection of Hantavirus and Arenavirus was carried out by Polymerase chain Reaction technique. Results. A total of 50 rodents were captured belonged to 3 families and six species, the Muridae (76%) with the highest number of captured individuals, Cricetidae (22%) and Echimydae (2%). All samples were negative for the molecular markers of Hantavirus and Arenavirus. Conclusions. The study of mammalian hosts, particularly small rodents contribute to monitor diseases transmitted by these small mammals that act as reservoirs.