Objective To investigate the carrying status of disinfectant resistance genes in clinically isolated carbapenem-resistant Klebsiella pneumoniae (CRKP) and the homology of strains that carried disinfectant resistance genes in Wuhan City, and provide theoretical basis for the effective prevention and control of CRKP transmission. Methods Non-repetitive CRKP strains isolated from hospitalized patients in three tertiary hospitals in Wuhan City from 2018 to 2019 were collected. Antimicrobial susceptibility were tested by minimum inhibitory concentration (MIC). Disinfectant resistance gene qacEΔ1 and cepA were detected by real-time polymerase chain reaction (RT-PCR). Homology of CRKP strains carrying both qacEΔ1 and cepA genes was analyzed by pulsed-field gel electrophoresis (PFGE). Results A total of 62 CRKP strains were collected, 77.42% were from intensive care unit (ICU), 40.32% were isolated from sputum specimens. All CRKP strains were multidrug-resistant, with resistance rates to ertapenem, amoxicillin/clavulanic acid, cefazolin, ceftazidime, and ceftriaxone being 100% and high resis-tance to other frequently used antimicrobial agents. The detection rate of disinfectant resistance genes was 95.16% (59/62), among which qacEΔ1 and cepA genes were 64.52% (40/62) and 91.94% (57/62), respectively, with 38 strains (61.29%) detected both qacEΔ1 and cepA genes. PFGE results showed that 38 CRKP strains can be divided into 11 types (from A to K), with type E being the major type, accounting for 42.11% (n=16). Conclusion Antimicrobial resistance of CRKP strains in Wuhan is severe. Strains carry disinfectant resistance genes widely. There is clonal transmission among different hospitals and departments. Epidemiological monitoring should be streng-thened, and disinfectant should be used rationally.