A total number of 100 random samples of raw milk and kareish cheese (50 for each) were collected from Assiut city farms and dairy shops. Shigella species were isolated, confirmed biochemically and by using Polymerase Chain Reaction (PCR). Also two virulence genes; invasive gene (invC) and plasmid- encoded virulence gene (ipaH) were identified using PCR technique. 10 isolated strains of Shigella isolates (37%) from dairy milk samples and 13 isolates (43%) from kareish cheese were identified as following: S. dysenteriae, S. flexneri, S. sonnei and S. boydii. The two virulence genes; (invC) and (ipaH) were detected in only six and four strains of the identified Shigella species, respectively. Four of them had both the virulence genes (isolated from milk and cheese samples). Even though conventional culture is considered the gold standard for Shigella detection and the PCR method is a useful tool which complements detection of foodborne pathogens such as Shigella. Chitosan was evaluated in this study as antibacterial substance on the identified Shigella strains by inoculating it in pasteurized milk, using 3 different concentrations: 0.25, 0.5 and 1% of chitosan. Chitosan reduced the inoculated Shigella strain mean counts with highly significant effect (P<0.01) at the 6^th day reached to 2.10 ±0.17, 1.00 ±0.30 and th day we noticed that chitosan concentration of 0.5% only was highly significant (P<0.05). Generally, the 0.5% chitosan concentration showed the highly reduction effect on the count and survival of the Shigella strain involved.