The genus Phlebovirus currently consists of 67 viruses. As established by the International Committee on Taxonomy of Viruses (ICTV), these viruses are classified using the amino acid sequence of RNA-dependent RNA polymerase (RdRp), considering more than one species when the percentage of identity is less than 95%. This genus comprises species that are considered of public health importance since they cause symptoms that can be confused with other diseases or can be fatal and are transmitted by hematophagous insects of the genus Lutzomyia in the New World, recognized vectors of Leishmania spp. In the present work, species of phlebotomine sandflies known for their anthropophilic activity, such as Lutzomyia evansi and Lutzomyia panamensis, were morphologically identified, in addition to detecting and phylogenetically characterizing a large part of the L segment of Phlebovirus by next-generation sequencing, which are grouped in the Aguacate complex that includes species known to be responsible for outbreaks of febrile disease in humans and animals. This sequence was used because RdRp is the most conserved and best characterized protein among members of the Phenuiviridae family. Specifically, the presence of Lu. evansi infected with a species of Phlebovirus, which is grouped in the Aguacate complex, is recorded for the first time in Colombia. This finding may be relevant in public health given its background and merits further research on vector ecology and the impact of the virus on human populations in the area.