| Summary: | <i>Yersinia pestis</i>, the etiological agent of the plague, is considered a genetically homogeneous species. Brazil is currently in a period of epidemiological silence but plague antibodies are still detected in sentinel animals, suggesting disease activity in the sylvatic cycle. The present study deployed an in silico approach to analyze virulence factors among 407 Brazilian genomes of <i>Y. pestis</i> belonging to the Fiocruz Collection (1966–1997). The pangenome analysis associated several known virulence factors of <i>Y. pestis</i> in clades according to the presence or absence of genes. Four main strain clades (C, E, G, and H) exhibited the absence of various virulence genes. Notably, clade G displayed the highest number of absent genes, while clade E showed a significant absence of genes related to the T6SS secretion system and clade H predominantly demonstrated the absence of plasmid-related genes. These results suggest attenuation of virulence in these strains over time. The cgMLST analysis associated genomic and epidemiological data highlighting evolutionary patterns related to the isolation years and outbreaks of <i>Y. pestis</i> in Brazil. Thus, the results contribute to the understanding of the genetic diversity and virulence within <i>Y. pestis</i> and the potential for utilizing genomic data in epidemiological investigations.
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