A genome sequence-based analysis of 74 carbapenem-resistant Klebsiella pneumoniae (CRKP) from 12 hospitals in Sichuan, China, revealed that the isolates carried blaKPC-2 (n = 48), blaNDM (n = 22), or blaIMP-4 (n = 4) were identified as K. pneumoniae (n = 67), Klebsiella variicola (n = 5), and Klebsiella quasipneumoniae (n = 2) and belonged to 19 sequence types. Both inter- and intrahospital transmission of multiple ST11 strains was identified. There is an urgent need for all hospitals in a given region to coordinate actions against CRKP.