The indicator bacteria are the gauge of the presence possibility of fecal substances which may relate to fecal pathogens and consider being responsible of food quality because they are not usually the cause of disease but sometimes related to foodborne organisms. In this research, sixty samples of milk products were collected from various areas in Port-Said city including Romi cheese (Ras/dry cheese), mozzarella cheese (shredded cheese), triangle cheese (processed cheese), Tallaga cheese (low salt/soft cheese) and feta cheese (tetrapacked cheese). Indicator bacteria were detected by the cultural traditional techniques (cultivation on general and selective media) and by advanced (PCR techniques) multiplex polymerase chain reaction. This study developed multiplex PCR targeting specific genes for differentiation of the most popular indicator bacteria and simultaneous detection for the bacteria which indicate the pathogen presence Escherichia coli (uidA), Enterobacter sp. (16S rRNA) and Enterococcus sp. (tuf) from targeted food samples. Generally, the 3plex-PCR assay revealed that the most common indicator found in most samples of milk products with high frequency was Escherichia coli which was distributed within most of the samples having the maximum occurrence frequency reached 60% followed by Enterobacter sp. reached 24% then Enterococcus sp. reached 16%. The aim of using rapid 3 multiplex polymerase chain reaction for detecting indicator bacteria in cheese samples is providing more food safety for consumers and rapid action against violating food suppliers.