Salad vegetables are the important sources of vitamins and minerals for human diet. However, salad vegetables are potential vehicles for non-typhoidal Salmonella spp. (NTS) as reported in our previous study. Such contamination posed significant food poisoning risk to consumer. The aims of present study include determination of the virulence genes prevalence in NTS isolates in samples from retail markets and farms. Besides, characterization of NTS isolates was performed to determine their genetic relatedness. Multiplex PCR assay was done to detect the presence of 15 virulence genes in 58 NTS isolates. The genetic relatedness of 33 NTS belonging to S. Weltevreden, S. Albany, S. Hvittingfoss, S. Aberdeen, S. Poona and S. Corvallis were characterized using ERIC-PCR and BOX-PCR typing methods. Results showed the presence of 13 virulence genes (spiA, pagC, msgA, invA, sipB, prgH, spaN, orgA, tolC, sitC, lpfC, sifA and sopB) among all the isolates with 53 (91.38%) isolates carried more than 11 virulence genes, while other five isolates carried the genes in the range of six to nine types. None of the isolates possessed spvB and pefA genes. Major clusters were observed at a genetic distance percentage of 90% for both ERIC- and BOX-PCR with discriminatory index of 0.917 and 0.873, respectively. In terms of source and type of sample, all NTS isolates were found diverse without clear association, thus no specific cluster was found. In summary, this study demonstrated the potential risks of NTS from salad vegetables to cause foodborne diseases and they were commonly found to be related with regard to their specific serovars.