Serotyping is the basis of Salmonella surveillance. However, the limitations of the traditional serotyping have stimulated rapid research and development in DNA-based serotyping. The aim of this study was to apply a combination of sequential multiplex PCRs targeting the O, H and Vi antigens to serotype a panel of 122 recently isolated human-and foodborne-Salmonella strains. The mPCR that targets the o (genes wzxC2, rfbJ, prt, tyv, wzxE, wzxC1, prt) and Vi (viaB) antigens successfully subtyped the strains into serogroups C2 (n = 35, 28.7%), B (n = 33, 27.1%), D9 (n = 29, 22.9%), E (n = 21, 17.2%), C1 (n = 2, 64%) and A (n = 2, 1.64%). Eight of the Salmonella strains from serogroup D were positive for Vi antigen. Two multiplex PCRs were optimized for detection of H1 antigens (Ha, Hb, Hd, r, z 10 , z 6 , g and m) and H2 antigens (1.5, 1.2, 1.6 and enx). Overall, the multiplex PCRs of O, H and Vi antigens results correctly serotyped 94 of 122 strains (77%). The most frequent serovars encountered were Salmonella weltevrerden, Salmonella enteritidis, Salmonella typhimurium, Salmonella hadar and Salmonella typhi. Application of DNA based technique for serogrouping and serotyping of the selected Salmonella enterica was found to be robust, quick, specific and reliable for the specific antigenic targets and is useful in the study area which lack complete serotyping facilities.