The current study was carried out to evaluate the current prevalence of the food-borne pathogen; Shigella spp., in local stored cheese in Al-Diwaniyah City, Iraq, by using the virulence ipaH and uidA genes as targets for molecular tools. The study included the bacterial cultivation of 450 local cheese samples (collected during June to September, 2022) utilizing conventional methodology. The recovered Shigella spp. isolates were subjected to a real-time PCR (RT-PCR) that focused on the genes mentioned above. The results of the cultivation revealed the presence of 110 (24.4%) Shigella spp. isolates in the examined cheese samples. The RT-PCR showed that the virulence genes were identified in 84 (76.4%) and 98 (89.1%), respectively, in the bacterial isolates, which indicated the existence of Shigella dysenteriae. The current findings indicate the presence of Shigella spp. in local cheese, which needs urgent control to eliminate the source of infection or contamination.