This report builds on recent serological evidence for the presence of hantavirus in northern Colombia by providing sequence-specific and phylogenetic data of hantavirus infections in wild rodents. From August 2007 to August 2008, 354 rodent specimens representing four families were collected in the northwestern Antioquia region of Colombia. Antibodies reactive to Sin Nombre virus and Maciel virus antigens by IgG enzyme-linked immunosorbent assay were found in 15 of 109 (14%) Cherries cane rats (Zygodontomys cherriei), the only sigmodontinae rodents captured. Lung tissue samples from 11 of the 15 seropositive rodents were RT-polymerase chain reaction positive for hantavirus RNA, using primers for the S and M genome segments. Eight of these amplicons were sequenced and phylogenetic analyses indicated RNA of a hantavirus closely related to Calabazo virus, previously found in Panama. This is the first report of the genetic characterization of a hantavirus in rodents in Colombia.