<p><i>Yersinia enterocolitica</i> is a Gram-negative pathogen frequently associated with swine and pork products. Despite its global importance, little is known about the genomic characteristics of <i>Y. enterocolitica</i> in Brazil. Furthermore, the antimicrobial resistance (AMR) in <i>Y. enterocolitica</i> has been associated to be driven by horizontal gene transfer, especially in environments with intensive antimicrobial use. This study aims to investigate the phylogenetic and population structure of <i>Y. enterocolitica</i>, and antimicrobial resistance and virulence gene distribution using genome sequences to compare isolates obtained in Brazil with other isolates deposited in online databases. In this study, a total of 998 high-quality genomes from <i>Y. enterocolitica</i> deposited in the National Center for Biotechnology Information (NCBI) were evaluated for pangenome using the Roary software with MAFFT for alignment. Pangenome analysis and phylogenetic inference were also performed on a subset of 837 genomes from isolates obtained from both pig and human. The analyses followed the procedures determined by ModelTest-NG. ABRicate with PlasmidFinder database, Virulence Factor Database (VFDB) and CARD database were used to investigate plasmid markers, virulence genes and resistance genes. Comparative analysis with international strains from public databases suggests that specific <i>Y. enterocolitica</i> strains circulate in Brazil. Swine and human isolates from Brazil were consistently grouped together, suggesting a strong zoonotic link. Additionally, the study underscores the correlation between antimicrobial use in pig farming and resistance gene prevalence. Our findings contribute to the understanding of <i>Y. enterocolitica</i> epidemiology in Brazil and emphasize the importance of genomic surveillance under the One Health approach to prevent foodborne diseases and combat antimicrobial resistance.</p>