Although the prevalence of the carbapenem-resistant (CRAB) has increased in Taiwan, few studies have elucidated the prevalence of different carbapenemase genes in Taiwan. The first objective of this study was to identify the types and prevalence of different carbapenemase genes, and the second objective was to determine the carbapenem antimicrobial susceptibility of carbapenemase producing isolates. In total, 269 CRAB blood isolates from four medical centres in Taiwan from 1/1/2009 to 31/12/2013 were analysed. Antimicrobial susceptibilities were determined using the Vitek 2 system. Carbapenemase genes were identified by polymerase chain reaction (PCR) and sequencing. Pulsed-field gel electrophoresis (PFGE) was used to identify the different pulsotypes. All 269 CRAB isolates had the -like gene, while 237 (88.1%) had the -like gene, and 11 (4.09%) had the -like gene. Twenty-one CRAB isolates (7.81%) contained only the -like gene. None of the isolates had the -like gene or the metallo-β-lactamases (MBL)-encoding genes. In 28.69% of isolates with the -like gene and 90.91% of isolates with the -like gene, the minimum inhibitory concentrations (MICs) for imipenem were 64 mg/L or more. In 37.55% of isolates with the -like gene and 100% of isolates with the -like gene, meropenem MICs were 64 mg/L or more. PFGE analyses indicated that six highly similar genomes which harbored the -like gene came from three different medical centres. Our study determined the prevalence of CRAB, the types and prevalence of carbapenemase genes, carbapenem susceptibility among CRAB isolates, and documented that the -like gene had greater resistance to carbapenem than the -like gene. We also demonstrated inter-hospital transmission of the highly resistant -like gene.