Abstract: Objective To understand the etiological and molecular epidemiological characteristics of a death case of meningococcal disease in Beijing in January 2013. Methods Cerebrospinal fluid (CSF) and blood samples were collected from the case for pathogen isolation. The isolated strain was detected with real-time fluorescence quota polymerase chain reaction (PCR) and multi locus sequence typing (MLST). Outer membrane protein PorA, FetA genes were detected to identify the isolated strain. Drug susceptibility test to 12 antibiotics was conducted. Results Specific gene ctrA of N. meningitidis and serogroup B-specific gene siaD were detected from the CSF and blood samples. One strain of N.meningitidis was isolated from CSF and no N. meningitidis strains were isolated from throat swabs of the close contacts. The isolate belonged to serogroup B according to bacteriologocal and serological detection results, which was supported by the results of PCR. The MLST analysis indicated that the sequence type of the isolate from the case was ST10051, belonging to ST4821 complex. The PorA and FetA alleles of the strain were P1.20,23-9 and F1-91 respectively. The strain was sensitive to 9 antibiotics except for trimethoprim-sulfamethoxazole,ciprofloxacin and tetracycline. Conclusion The isolate reported had a phenotype of B: P1.20, 23-9: F1-91:ST-10051 (cc4821) which is high pathogenic and had caused infection even death. It is necessary to fully understand the carriage and infection status of N. meningitidis in Beijing.