A bout of twenty isolates of Shigella species were isolated and identified from 200 stool speciments of patients suffering from diarrhea where S. flexneri was 3 (15%), S. Sonnei 4(20%), S. dysenteriae 13(65%) and S. boydiii 0(0%). The genomic DNA of these isolates was extracted using genomic DNA kit and the concentration and the purity of DNA were measured. The antibiotic susceptibility tests, showed that there were significant difference (P≤0.05) among the species of Shigella and the extended-spectrum B-lactamase (ESBL) genes. It was found that 76.6 % and 44% of the isolates were susceptible to ciprofloxacin and ceftriaxone, respectively. All of the isolates were resistant to ampicillin, 45% to nalidixic acid, 55% to ceftriaxone, 15% to ciprofloxacin, 60% to chloramphenicol and cefixime, 65% to ceftazidime and 40% to gentamicin. The antibiotics resistance and ESBL genes in Shigella spp. isolates revealed a harmony relationship between them. The resistance rate to most antibiotics was observed in the isolates of blaCTX-M gene, the isolates of blaCTX-M gene were resistance to all antibiotics, the isolates of blaTEM, blaSHV and blaAMPC genes were resistance to ciprofloxacin (66.66%) and the isolates of blaSHV genes were resistance to chloramphenicol (25%) and ceftriaxone (27.27%). This study indicated that Shigella spp. are one of the main causes of diarrhea and their resistance to antibiotics was due to the presence of ESBL genes.