Several techniques were developed for identifying and quantifying Perfluorinated alkyl substances (PFASs). However, high cost, tedious procedures for separation before analysis and limited sensitivity are the limiting constraints of the existing PFAS sensors. Hence, there is a need to develop simple, low-cost and effective sensors for detecting emerging pollutants called perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS). An attempt was made to develop genetically modified bacterial biosensor system for the detection of PFOA and PFOS in water samples. The biosensor response was achieved from 10 ng/L to 10 ppm of PFOA and PFOS compounds with 24 h incubation time. The biosensor was successfully applied for the detection of PFOA or/and PFOS in different water samples and the results agree well with those results obtained by liquid chromatograph-mass spectrometer. Therefore, the developed biosensor system can be utilized for monitoring PFOA and PFOS compounds in the water samples such as pond, Lake, River and wastewater.