Background: Klebsiella pneumoniae is a major cause of infections and reproductive disorders among horses, ranked in recent French studies as the sixth most frequently isolated bacterial pathogen in equine clinical samples. Multidrug Resistant (MDR) K. pneumoniae strains are considered a major global concern by the World Health Organization, including the veterinary medicine. Objectives: To (i) characterise by a genomic approach 119 equine K. pneumoniae strains responsible for various manifestations of infection, (ii) describe the main antibiotic resistance profiles and acquired resistance genes, and (iii) describe the proportion of virulence genes. Study design: In vitro analysis of microorganisms. Methods: 119 equine K. pneumoniae strains collected between 1996 and 2020, from necropsies, suspected bacterial infections (mainly genital) and contagious equine metritis analyses were studied. Antimicrobial susceptibility profiles were determined using 35 molecules by disk diffusion method. After Illumina sequencing, in silico analyses were performed including species identification, MLST, cgMLST, genetic determinants identification: O-antigen, K-antigen (compared with multiplex K125 PCR), virulence genes, antibiotic resistance genes, plasmid types. Results: A wide genomic population diversity was observed and highlighted 39% MDR and 9% hypervirulence including 5% MDR-hypervirulent strains. An increase in resistance to 29 antibiotics was observed for necropsy-associated strain isolations during the period 2008–2020 compared with 1996–2007. Main limitations: Retrospective study including two distinct but complementary sources of equine K. pneumoniae strains. Conclusions: These findings emphasise the importance of improving the surveillance of K. pneumoniae in equine diagnostic tests to detect high-risk MDR-hypervirulent K. pneumoniae strains, which are currently not detected by the simple K1, K2 and K5 serotype approach.[1] Ethical animal research: Not required: analysis of microorganisms. Informed consent: Not applicable. Competing interests: None declared. Funding: The French Horse and Riding Institute, IFCE (http://www.ifce.fr) and GIS CENTAURE Recherche Equine, and internal research fund ANSES and DYNAMICURE UMR1311. Reference: [1] Gravey F, Sévin C, Castagnet S, Foucher N, Maillard K, Tapprest J, Léon A, Langlois B, Le Hello S, Petry S. Antimicrobial resistance and genetic diversity of Klebsiella pneumoniae strains from different clinical sources in horses. Front Microbiol. 2024;14:1334555. doi: 10.3389/fmicb.2023.1334555.