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<i>Klebsiella pneumoniae</i> is an opportunistic pathogen with various virulence factors that give it the capability to invade a host. Nevertheless, the treatment of bacterial infection is gradually complicated as the bacteria can develop resistance to antimicrobial agents. As nanotechnology is a prosperous field for researchers, we employed zinc oxide (ZnO) nanoparticles (NPs) on isolates of <i>Klebsiella pneumoniae</i>. Here, we studied the effect of three NP concentrations—0.25, 0.50, and 0.75 mM—on the gene expression of <i>Klebsiella pneumoniae</i> capsules in isolates collected from different samples. After conducting an anti-bacterial test, the highest nine types of bacteria that resisted the antibacterial agent were chosen for further examination. The gene expression of four genes responsible for capsule manufacturing, namely <i>magA</i>, <i>k2A</i>, <i>rmpA</i>, and <i>kfu</i>, were investigated. When the NP concentration was 0.25 mM, the lowest efficiency was obtained. However, when the concentration increased to 0.50 mM, a noticeable effect on gene expression was detected; consequently, at a concentration of 0.75 Mm, the highest impact was achieved and the gene expression was stopped.