Comprising 19 species/subspecies, Yersinia are Gram-negative coccobacilli implicated in a variety of human and zoonotic diseases. Several species of Yersinia share high genomic similarity with each other, and the ability to discern these species is vital—particularly for Y. pestis, the causative agent of plague, whose genomic composition is closely related to Y. pseudotuberculosis. In this study, we aim to revisit the taxonomy of Yersinia through whole-genome sequencing (WGS) of the type strains and confirm their taxonomic assignment. Whole-genome distances and phylogenomic analyses confirmed the current taxonomy of 17 species/subspecies. Unsurprisingly, four species that showed a greater degree of relatedness are Y. pestis, Y. pseudotuberculosis, Y. similis, and Y. wautersii, which constitute the Y. pseudotuberculosis complex. Recent research using multilocus sequence analysis identified Y. wautersii as a novel member species of the Y. pseudotuberculosis complex. However, based on whole-genome distances, our data shows enough similarity between Y. wautersii and Y. pseudotuberculosis to be considered the same species but different subspecies. Phylogenomic trees, which place Y. wautersii and Y. pseudotuberculosis on the same branch, further substantiate this data. We propose the unification of Y. pseudotuberculosis and Y. wautersii as Y. pseudotuberculosis subsp. pseudotuberculosis and Y. pseudotuberculosis subsp. wautersii, respectively.