Among the Cronobacter genus, Cronobacter sakazakii is the most common species posing a severe health risk for newborns, infants and children. Some infant formulas, cereal-based foods, and food production environments may be the potential reservoirs of C. sakazakii. This pathogen possesses different virulence factors encoded by different virulence genes. Therefore, characterizing these genes is important for distinguishing pathogenic strains from nonpathogenic ones. The objective of this study was to characterize some virulence genes [OmpA, OmpX, zpx, and Cpa] by real-time polymerase chain reaction (PCR) in C. sakazakii isolates from a total of 120 samples (20 each of milk powder, starch, rice flour, semolina, infant formula and dust samples from food production environments). Overall, 13 isolates (7 from milk powder, 2 rice flour, 1 semolina, and 3 dust) were cultured, identified by bioMérieux API® 20E test kit, and then subjected to real-time PCR application for screening the target virulence-associated genes. Our results showed that all of 13 isolates were positive for the virulence genes OmpA, OmpX, zpx, and Cpa. In summary, our study revealed that some of the analyzed foods and environmental samples were contaminated with pathogenic C. sakazakii with its virulence-associated markers, far above the allowable limit; and therefore, this level of contamination may pose a severe health threat for newborns, infants, and children.