Multi-drug-resistant bacteria, particularly Methicillin resistant, have become an ever-increasing problem. Currently, broad spectrum antibiotics are prescribed until bacteria can be cultured, a process that can take 3-4 days and is unable to deliver quantitative information about relative number of bacteria present. In order to rapidly detect, differentiate and quantify bacteria in blood samples we designed a detection system using labeled bacteriophage in conjunction with photoacoustic flow cytometry. Photoacoustic Flow cytometry is the generation of ultrasound waves created by the absorption of laser light in objects under flow. Bacteria can be tagged with dyed phage and processed through the photoacoustic flow cytometer where they are detected by the acoustic response. Here we demonstrate that E.coli can be detected and discriminated from Salmonella using this method.