The genus of Salmonella is very polymorphic and comprised of a number of genetically closely related serotypes. It is one of the emerging pathogen in food-borne disease which is often found in contaminated chicken eggs. Salmonella enterica is considered one of the major pathogens in public health worldwide. A total of 31 Salmonella isolates identified by specific antisera, which included Salmonella enteritidis (51.6%), Salmonella typhimurium (25.8%), Salmonella infantis (19.4%) and Salmonella colindale (3.2%). DNA was extracted using phenol- chloroform- isoamylalchol method. All the isolates showed fliC gene (1500bp) by using specific primers. PCR products were subjected to digestion using HhaI restriction endonuclease. PCR- RFLP results showed 3 patterns between all isolates. Our research gained in this study demonstrated that using HhaI restriction endonuclease could differentiate Salmonella enteritidis and Salmonella colindale but there is similarity between pattern of Salmonella typhimurium and Salmonella infantis.