Aptamers are simple DNA or RNA sequences selected by SELEX procedures. These recognition elements exhibit efficacy across a wide range of analytes. In recent decades, there has been an increasing interest in the detection of bacteria by aptamers with the aim of developing new therapeutic and diagnostic tools. Numerous sequences targeting various bacteria have been reported in the literature. In this study, the interactions between aptamers/antibodies targeting Escherichia coli strains (ATCC 700728 and 8739) were investigated in detail using both direct (flow cytometry) and indirect (fluorescence spectroscopy) methods . Many assays were carried out by varying several parameters such as the concentration of aptamers/antibodies, concentration of bacteria, nature of the buffer, temperature, and incubation time to find the optimal conditions to obtain the best interaction. Specificity studies were undertaken using two control strains (an untargeted Escherichia coli and a Staphylococcus epidermidis) and the Minimum Inhibitory Concentrations (MICs) of the aptamers against the bacteria tested were assessed. Observing interactions through an indirect method has proven to be challenging due to the very low specific surface area of the cells and to the presence of intracellular content in the media . Conversely, employing flow cytometry demonstrated that this method is more suitable to study the interactions between bacteria and biomolecules. The main asset of flow cytometry is its rapid and direct detection, also the sample can be analysed immediately after incubation without treatment. However, in that case, the data processing method may impact the study's conclusions. Finally, based on our results, the advantages, and the limitations of aptamers/antibodies as recognitions elements for bacteria was discussed .