Escherichia coli (E. coli) is one of the most frequent opportunistic pathogens. We aimed to carry out this study on antimicrobial resistance pattern and phylogenetic background of E. coli isolated from children who have diarrhea in different hospitals of the Iraqi Kurdistan region. A total of 200 fecal samples of children (52.5% male and 47.5% female) were included. Stool samples were cultured on selective media to isolate E. coli bacteria. The antibiotic susceptibility testing and molecular characterization of the isolates were carried out. Antimicrobial susceptibility testing was performed by disc diffusion test disc PCR was used to detect five antimicrobial resistance genes coding for β-lactamases (blaTEM, and blaCTX, blaOXA, blaSHV, blaCMY) to study phylogenetic grouping of E. coli. The Escherichia coli were highly resistant to β-lactam antibiotics, and the highest resistance was seen to Cefotaxime (45.4%). According to the phylogenetic grouping of E. coli isolates, group B2 was the dominant group and blaOXAgene (57.5%) was the predominant resistance genes among E. coli isolates. This study demonstrated the clinical concern of E. coli in children. The E. coli are highly resistance to common beta-lactam antibiotics and there are high rates of the resistance genes among E. coli isolates in children. An antibiotic surveillance would be useful continuously control and prevention of infectious diarrhea in children.