Currently, Salmonella enterica is the most common bacterial foodborne pathogen, causing serious extraintestinal disease. Typing methods play an important role on pathogens’ source tracking, knowing the source(s) of bacteria in pharmaceutical sciences, preventing and controlling the diarrhea and food-poisoning outbreaks. The purpose of this study is to use different moleculer typing methods to determine the genetic variability of 38 foodborne Salmonella isolates that were previously identified by biochemical tests. The methods were evaluated by four molecular techniques including 16S rRNA sequencing, PFGE, PCR-RFLP and invA-spvC PCR. 16S rRNA sequencing results showed that four of the 38 isolates were Escherichia coli, Proteus mirabilis and Citrobacter murliniae, and the others were Salmonella enterica. Thirty-eight strains were subtyped by XbaI-PFGE into 20 profiles with different clusters, while they were subtyped by 16S rRNA-RFLP into 9 profiles with a single cluster. Out of two Salmonella isolates, the invasion gene (invA) was detected in all other Salmonella isolates (94%) and the virulence gene (spvC) was detected in 11% of Salmonella isolates. Our results suggested that the PFGE subtyping is the prominent method for the evaluation and benchmarking of molecular subtyping.