Listeria monocytogenes is a globally relevant foodborne pathogen and a major public health concern because of its ability to cause severe invasive disease and persist in food processing environments. This study aimed to characterize the genomic diversity of L. monocytogenes isolates collected in Uruguay from food and clinical cases of listeriosis between 2010 and 2019. The genomes sequences of 142 isolates representatives from a national collection were obtained and used for comparative genomic and phylogenetic analysis along with other 55 genomes from different geographical regions. The isolates belonged to lineages I (88%) and II (12%) and were distributed across 20 clonal complexes. The clonal complexes CC3, CC2, and CC1 were predominant. Notably, CC3 accounted for nearly one third of the isolates and was evenly distributed between food and clinical sources, contrasting with its relatively low frequency in most international datasets. A novel sequence type (ST2832) and 112 new core genome MLST profiles were identified. The circulation of the rare clonal complex CC517 was detected, with evidence of persistence in food environments and a potential link to a human case. Comparative analysis revealed considerable virulence gene diversity, including specific distribution of LIPI-3 and LIPI-4 among lineages and clonal complexes, and the presence of truncated allelic variants of the inlA gene in food-derived lineage II isolates. Phylogenetic analysis showed strong concordance with MLST-based classification and reveals linkage among isolates form different sources suggesting epidemiological relation between food and human cases of listeriosis. This study provides the first comprehensive genomic overview of L. monocytogenes in Uruguay, revealing the predominance of lineage I isolates from food and clinical sources, a particular high prevalence of CC3 and the local circulation of the rare CC517. The results highlight the importance of whole genome and phylogenetic analysis as molecular epidemiology tools and show the contribution of including isolates from underrepresented regions in global genomic databases.