Salmonella enterica serotype Enteritidis (S. Enteritidis) is an important causative agent of nontyphoidal salmonellosis in human populations. In this study, we collected 72 S. Enteritidis strains from 2004 to 2014 in Ningbo, mid-east China. Of the 72 strains, we identified a dominant clone of 58 strains recovered from patient's feces (n = 48), blood (n = 1), pleural effusion (n = 1), chickens (n = 3), and dessert cakes (n = 5) by pulsed-field gel electrophoresis (PFGE) and variable-number of tandem repeat analysis (MLVA). The profile arrangements of MLVA were SE1-SE2-SE3-SE5-SE6-SE8-SE9: 4-4-3-11-10-1-3. These dominant strains were susceptible to ampicillin, chloramphenicol, tetracycline, ciprofloxacin, gentamicin, cefotaxime and trimethoprim-sulfamethoxazole, and resistant to nalidixic acid. Additionally, all isolates harboured virulence genes invA, sipA, sopE, and spvB when tested by PCR. Our results reveal that genetically similar S. Enteritidis strains which accounted for several outbreaks as well as blood infection and pleural cavity infection are prevalent in China for a long-term period. This situation calls for further attention in the prevention and control of foodborne disease caused by Salmonella species.