This mini-review focused on the current advances in the development and the application of the antibacterial agents produced from probiotics strains against foodborne pathogens. Inhibitory activity of the pathogen growth could be achieved by co-culture with probiotics and/or the treatment of metabolites extracted from probiotics culture, whereas strain-dependent efficacy was mainly reported according to the bacterial species of the target pathogens. To overcome the limited antibacterial spectrum and the efficacy of the metabolites from probiotics, the recent research highlight the discovery of novel bioactive substances with broad range of the inhibitory activity of foodborne pathogens and mode-of-action which has not been reported as the major research goal. Moreover, understanding the distribution of functional and regulation genes coding the production of the antibacterial metabolites based on the bacterial genome analysis can provide the clues for the mechanisms of the pathogen control by using probiotics. Major strategies on the application of the genomics in this research area can be represented as follows: 1) functional annotation specialized for antimicrobial proteins, 2) assessment of the antibacterial effects followed by the general/functional annotation, 3) genome and metabolites analysis for the purification of antimicrobial proteins, 4) comparative genomics and the characterization of antimicrobial potential. Especially the relationship between phenotype-genotype based on genomic bioinformation with the results of the practical efficacy tests of bacterial metabolites as an active substance of disinfectants and/or preservatives can be expected to act as supportive research for broadening our knowledge regarding the key metabolic pathways associated with the production of antibacterials from probiotics.