The Gram-negative bacterium Klebsiella pneumoniae is a major human health threat underlying a broad range of community- and hospital-associated infections. The emergence of clonal hypervirulent strains often resistant to last-resort antimicrobial agents has become a global burden as treatment options are limited. The Kingdom of Saudi Arabia (KSA) has a dynamic and diverse population and serves as a major global tourist hub facilitating the dissemination of multidrug-resistant (MDR) strains of K. pneumoniae. To examine the spread of clinically relevant Klebsiella pneumoniae strains, we characterized the population structure and dynamics of multidrug-resistant K. pneumoniae across the KSA hospitals.