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Simple Summary: Understanding the genetic makeup of microorganisms provides information on their evolutionary relationship with other similar organisms. It also sheds light on their ability to cause disease in susceptible individuals and to resist the hosts' defense mechanisms, including the effects of antimicrobial therapy. In this study, we performed complete genome sequencing and characterization of bacteria called Arcanobacterium hippocoleae, which were isolated from the reproductive tract of infected mares. These bacteria displayed small and large phenotypes when grown on artificial media. The whole genome sequences between the large phenotypes were closely related, while the small and large types were distant from each other in terms of sequence size and identity. Putative genetic elements that might be associated with disease conditions were identified in both bacterial phenotypes. Several genes that express hypothetical proteins with unknown functions were also detected. This study provides the complete genetic structure and analysis of different phenotypes of Arcanobacterium hippocoleae and will serve as a benchmark for future studies to identify the potential function and role of the bacterial proteins in the ability of the bacterium to produce reproductive tract diseases in mares. Arcanobacterium hippocoleae is a Gram-positive fastidious bacterium and is occasionally isolated from the reproductive tract of apparently healthy mares (Equus caballus) or from mares with reproductive tract abnormalities. Apart from a few 16S rRNA gene-based GenBank sequences and one recent report on complete genome assembly, detailed genomic sequence and clinical experimental data are not available on the bacterium. Recently, we observed an unusual increase in the detection of the organism from samples associated with mare reproductive failures in Atlantic Canada. Two colony morphotypes (i.e., small, and large) were detected in culture media, which were identified as A. hippocoleae by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Here, we report the whole genome sequencing and characterization of the morphotype variants. The genome length of the large phenotypes was between 2.42 and 2.43, and the small phenotype was 1.99 Mbs. The orthologous nucleotide identity between the large colony phenotypes was ~99%, and the large and small colony phenotypes was between 77.86 and 78.52%, which may warrant the classification of the two morphotypes into different species. Phylogenetic analysis based on 16S rRNA genes or concatenated housekeeping genes grouped the small and large colony variants into two different genotypic clusters. The UvrA protein, which is part of the nucleotide excision repair (NER) system, and 3-isopropoylmalate dehydratase small subunit protein expressed by the leuD gene were identified as potential virulence factors in the large and small colony morphotypes, respectively. However, detailed functional studies will be required to determine the exact roles of these and other identified hypothetical proteins in the cellular metabolism and potential pathogenicity of A. hippocoleae in mares. [ABSTRACT FROM AUTHOR]