The poor hygiene practices during the making and distribution of indigenous cheese, milk and its products can pose a health threat to the community, especially kids, due to the existence of dangerous bacteria like Shigella and E. coli. In Qualubia Governorate, a total of 135 samples were collected randomly, including stool from children with diarrhea, raw cow's milk, and kareish cheese (45 of each type). A sum of 8 Shigella flexneri and 31 E. coli strains were detected and confirmed using multiplex PCR. The ipaH and lacY genes, were discovered to have a length of 619 bp and 101 bp each, respectively. Although traditional culture is the preferred method of identifying foodborne pathogens such as Shigella and E. coli, the PCR method is also useful for confirming them. Antibiotics have revolutionized our approach to treating common bacterial infections. Overuse and incorrect use of antibiotics to treat diarrhea can lead to increased antibiotic resistance. Invitro sensitivity tests on 31 isolated E. coli strains showed high resistance to ampicillin (90.3%), nalidixic acid (90.3%), amoxicillin (87.1%), and cefatixime (77.4%). The resistance rates of the 8 Shigella strains were 87.5% for amoxicillin and ampicillin, 75% for nalidixic acid and tetracycline, and 62.5% for cefotaxime. Multiplex PCR was utilized to identify various resistance genes in E. coli and Shigella strains including blaTEM, blaCXTM, blaSHV, blaOXA, gyrA, parC, tetA (A), and sul1 genes found at 445 bp, 593 bp, 237 bp, 813 bp, 648 bp, 395bp, 570 bp, and 433 bp lengths, respectively.