<jats:p><jats:italic>Klebsiella pneumoniae</jats:italic>is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections.<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>into three distinct species, KpI (<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>), KpII (<jats:italic>K</jats:italic>.<jats:italic>quasipneumoniae</jats:italic>), and KpIII (<jats:italic>K</jats:italic>.<jats:italic>variicola</jats:italic>). Further, for<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>(KpI), the entity most frequently associated with human infection, we show the existence of &gt;150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive<jats:italic>K</jats:italic>.<jats:italic>pneumoniae</jats:italic>infections; our data provide the whole-genome framework against which to track the emergence of such threats.</jats:p>