The current investigation focused on 13 Shigella isolates. These isolates were derived from 260 randomly sampled specimens including beef, chicken meat, cow's milk, and diarrheic child stool (with 65 samples each). The samples were collected from diverse sources such as butcher and poultry shops, supermarkets, and hospitals in Kaliobia Governorate, Egypt. The study's objectives encompassed the genetic identification of the isolates, analysis of their antimicrobial sensitivity profiles, and the determination of specific antimicrobial resistance genes. The results revealed pronounced resistance to amoxicillin, then ampicillin, tetracycline, nalidixic acid, streptomycin, and cefotaxime. Conversely, heightened sensitivity was observed towards meropenem, norfloxacin, gentamicin, and ciprofloxacin. Notably, all isolates exhibited resistance to a minimum of three distinct antimicrobials, categorizing them as multi-drug resistant (MDR).Genetically, all five studied Shigella isolates were Shigella species as all of them had ipaH gene of Shigella genus, the isolate No. 1, was S. sonnei strain as it carried the wbgZ gene of S. sonnei and the other four isolates were confirmed as S. flexneri strains as they had the ipaH1 gene of S. flexneri. Moreover, β-lactam resistance gene, blaTEM; quinolones resistance gene, qnrA and streptomycin resistance gene, aadA1 were amplified in all five studied Shigella strains giving products of 516 bp.; 516 bp. and 484 bp., respectively. Therefore, this study concluded that, these isolates (S. flexneri and S. sonnei) are MDR to three or more antimicrobials of public health importance and there is correlation between antimicrobial resistance phenotypes and genotyping of Shigella isolates.