Background and aims: The food-borne pathogens appear to be a reemerging and endless problem in the human community all over the world. Hence, all the outbreaks should be constantly monitored for pandemic strains and new mutant genotypes. The main purpose behind the molecular typing methods is the comparison of bacterial isolates to obtain genomic relatedness regarding epidemiological aspects. One of these methods that have been recently reported in several Iranian studies is pulse field gel electrophoresis (PFGE). The aim of this study was to review and discuss the current situation and difficulties, and also the necessity of planning for tracking new and re-emerging food-borne pathogens investigating PFGE future status in Iran as a molecular epidemiology tool. Results: According to the results, it was found that this technique requires high investments in both fields of required equipment and software some of which are now available in many research centers. In addition, investigations on various medical search engines revealed that hundreds of studies have been published after 2010 in Iran. These reports indicated that most of these studies were not able to provide an efficient epidemiological analysis of the outbreaks and prevention of future events, except for a few exceptions. Conclusion: A review of the capabilities available in the country in this respect led the researchers to infer that it may be the best time to make a plan on the existence of a general network of collecting and analyzing the results, as well as integrating them into the international databases. It is expected that these responsible institutions to make the required design in this field.