Proposal of a molecular protocol integrating two qPCR formats (targeting opr L and gyr B/ ecf X genes) for an early detection of Pseudomonas aeruginosa in sputum samples of patients with cystic fibrosis. The oprL qPCR is applied in screening because of its good sensitivity. In case of a doubtful or a positive result, the gyrB/ecfX qPCR is applied in a second time. Interpretation of the gyrB/ecfX qPCR takes into account the quantification found with oprL qPCR. Below the detection threshold of 730 CFU/mL, the oprL qPCR prevails over the gyrB/ecfX qPCR. Conversely, beyond this threshold, the gyrB/ecfX qPCR prevails over the oprL qPCR.