In this work, a comparative study using atomic force microscopy (AFM) and field emission–scanning electron microscopy (FESEM) has been carried out to assess the morphology of single cellEscherichia colibacteria (E-coli).E-colibacteria are a major concern for public health. Attention was focused on the certain strains ofE-colibacteria, because some strains can be toxic and cause food poisoning. TheE-colibacteria have attracted much research interest because this bacterium is easily to get, cheap and rapid reproductively. Imaging ofE-colirecently, was improved by using high resolution microscopy. Current techniques for detection such as, AFM and FESEM has attracted great interest and emerging as a potentially powerful whole-organism fingerprinting tool for the rapid identification of bacteria. The obtained results of AFM and FESEM techniques have been compared to show the image quality of single cellE-coli.