Motivation for the study. The role of bats as hosts of Trypanosoma spp. in the Atlantic department in Colombia, as well as its taxonomic diversity has been poorly studied. Main findings. This is the first report of frequency of infection by Trypanosoma spp. in bats in the Atlántico Department in Colombia. Implications. The great adaptive capacity of bats to different ecological niches and its role as hosts of Trypanosoma spp. for wild and urban ecotopes represents a risk factor in transmission cycles of epidemiological importance. We conducted a study to evaluate the frequency of infection by Trypanosoma spp. in bats captured in wild and urban ecotopes in the Department of Atlántico in the Caribbean region of Colombia from March 2021 to May 2022. Bats were taxonomically identified, and sex, relative age, and reproductive conditions were determined. A blood sample was used for parasitological analysis and DNA extraction to amplify a region of the 18S rRNA. 125 bats were collected, with the most abundant families being Molossidae (62/125; 49.6%) and Phyllostomidae (43/125; 34.4%). Molossus molossus collected in wild habitats showed an infection frequency of 8.1% (5/61) and 4.1% (3/61) through parasitological and molecular analysis, respectively. In comparison, Noctilio albiventris collected in urban habitats showed an infection frequency of 16.6% (2/12) for both analyses. These findings represent the first records of M. molossus harboring trypanosomes for the Department of Atlántico and of N. albiventris harboring trypanosomes in Colombia.