The need for alternative approaches for identifying pathogens has led researchers to focus on nanobiotechnology. In this study, zinc oxide nanoparticles (ZnO NPs) and multi-wall carbon nanotubes (MWCNTs) were used as marker molecules. After measuring the best concentration of these nanomaterials to inhibit the lactase activity of the beta-galactosidase enzymes by binding to them, different concentrations of Escherichia coli were added to the medium and their detection ability was finally compared with each other. Due to small size and high reactivity, these compounds are able to detect very low amount of bacteria in the ambient. In fact, the bacteria are attached to the nanoparticles and detach them from the enzyme and lead to substrate decomposition by the enzyme. MWCNTs exhibited better performance than ZnO NPs in detection of bacteria at very low concentration of 10(1) CFU/ml in 15 min. As a result, they are very appropriate to be utilized especially in the food industry.