Canine babesiosis is a disease produced by members of a group of protozoa of the Apicomplexa phylum called Babesia, among which the type canis is reported. In literature, three different subtypes have been described: Babesia canis canis, Babesia canis rossi and Babesia canis vogeli. Colombia, due to its tropical conditions, is favorable for the dissemination of the vector that uses the dog as a host. The traditional diagnostic approach is based on the identification of the parasite in blood smears; nevertheless, there are reports on variations in the genetic characteristics between strains, which may influence its pathogenic capacity and the specificity of the vectors. The objective of this study was to detect and characterize sequences of Babesia canis in blood samples of canines with a presumptive diagnosis of hemoparasitism, through the use of molecular tools. For this study, an intentional sampling of 22 blood samples was made. These samples were taken in Ibagué (Colombia), where the canines tested were suspects of hemoparasitism and subject to molecular evaluation for Ehrlichia spp. At PCR, three positive samples were detected (13,6%), two presented with co-infection with Ehrlichia spp., and one was infected with Babesia. After sequencing, the products showed 99% similarity with isolations of Babesia canis vogeli from Venezuela (DQ297390.1), Spain (DQ439545.1), Brasil (EU436752.1), China (KJ939326.1) and Sudan (DQ111766.1). This study confirmed the presence of Babesia canis vogeli in Ibagué, which fortifies the available information about the parasite in the country; nevertheless, more investigation is needed, especially on other hemoparasites causing similar symptoms.