With the increasing incidence of Salmonella enterica serovar Enteritidis (SE) infections, five SE foodborne outbreaks were identified between 2008 and 2010 on Jeju Island, Republic of Korea. In this study, the genetic relatedness of isolates recovered from the five outbreaks was investigated to identify the source of foodborne SE infections. In total, 57 SE isolates from five outbreaks (17 isolates, 5 isolates, 18 isolates, 8 isolates, and 9 isolates, respectively) were used for antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multiple-locus variable-number tandem repeat analysis (MLVA). SE isolates from 2008 and 2009 were resistant to nalidixic acid, whereas SE isolates from 2010 were resistant to five antibiotics. Of the five outbreaks, outbreaks A, B, and D had identical PFGE-XbaI and PFGE-BlnI patterns, SEGX01.003 and SEGA26.001, respectively. Outbreak C had patterns SEGX01.011 and SEGA26.005, and outbreak E had patterns SEGX01.007 and SEGA26.007. However, MLVA profiles further distinguished the SE isolates from each outbreak into patterns SEGM.014 (outbreak A), SEGM.012 (outbreak B), SEGM.008 (outbreak C), SEGM.016 (outbreak D), and SEGM.015 (outbreak E). Among these five outbreaks, three outbreaks were presumed to be caused by the clonal SE isolates depending on PFGE pattern, but the MLVA results elucidated that these were caused by different SE isolates from the different origins. Therefore, for the epidemiological investigation or surveillance of SE foodborne diseases, both PFGE and MLVA should be used together.