Abstract: Objective To analyze the discriminatory ability of pulsed-field gel electrophoresis (PFGE) and multi locus variable number tandem repeat analysis (MLVA) in molecular typing of Salmonella enteritidis isolates in China and establish a standard MLVA typing protocol and a subtyping database of S. enteritidis. Methods With the application of standard PFGE and MLVA protocols from PulseNet International network, the molecular typing of 289 isolates of S. enteritidis from 6 provinces in China was condcuted. The respective discriminatory power of the two assays were evaluated combined with the epidemiological information of the strains. Results The chromosomal DNA prepared from each S. enteritidis strain was digested with XbaⅠrestricted endonucleotidase and 55 PFGE patterns were observed. The discrimination index (D) was 0.8433 for PFGE typing. The predominate patterns of PFGE were JEGX01.CN0003 (35.6%) and JEGX01.CN0001(25.6%) respectively, and the major MLVA type ST1 was detected in 97 S. enteritidis isolates (37.5%) distributed in all provinces in different years, indicating that the discriminatory ability of MLVA was higher than PFGE . When PFGE and MLVA were integrated, 104 variant patterns were obtained and the D value reached 0.9058. For some strains from outbreaks, several clusters were detected through PFGE and MLVA analysis, but these strains could be distinguished completely from the sporadic strains detected during the same period. Conclusion The discriminatory powers of MLVA and PFGE are low for S. enteritidis. It is necessary to conduct PFGE and MLVA analysis in epidemiological survey to confirm the outbreak caused by S. enteritidis.