Brucellosis is a commonly diagnosed zoonosis that causes infertility and abortion in cattle, it is acquired from handling of infected animals or consuming contaminated milk or milk products. In Colombia, it is classified as prevention and control disease, despite its relevance little is known about the origin, epidemiology and the genetic constituents of the strains circulating in dairy farms. Here we present the draft genome of B. abortus Col-B012, an isolate obtained from a female Holstein belonging to a dairy farm in Nariño, Colombia. This genome comprises 3,234,714 bp and 3,018 predicted protein-encoding genes. Using comparative genomics and phylogenetic analysis, we found that the strain Col-B012 clustered with known biovar 4 variants. The analysis of the core genes allowed the identification of polymorphisms only present in biovar 4 genomes, these alleles might be associated with the phenotypic and pathogenic characteristics of the group and are proposed as possible targets for identification by PCR. The sequencing of B. abortus Col-B012 genome provides important insights to improve the diagnosis and the epidemiology of this disease and represents the first report of the biovar 4 in Colombia.