Microorganisms growing in biofilm phenotype are the cause of chronic infections. Several universal properties of biofilm communities are they are overwhelmingly polymicrobial, difficult to culture (viable but not culturable), and the individual constituents are very tolerant of antimicrobial agents, especially antibiotics. Just like in medical imaging utilizes multiple technological platforms such as ultrasound, magnetic resonance or x-ray, microbial identification requires multiple technologies and methods. However, when dealing with biofilm phenotype microorganisms, molecular methods are superior. Molecular methods have the ability to identify microorganisms with very high sensitivity, specificity and also can be quantitative. Utilizing a quantitative PCR methodology, specific targets can be identified as present/not present but also an absolute quantitative determination for each target present can be made. This allows for the determination of “bacterial load”. Sequencing platforms can reveal crucial relative quantification of the different microorganisms present, allowing for the determination of dominant microbes. Timely and accurate diagnostic information of microorganisms, which are the primary cause of the chronic infection, are essential for improving outcomes. PCR information can be returned rapidly, allowing the clinician to rule out antibiotic resistant microbes which allows for the selection of appropriate empiric antibiotics. Sequencing data, which returns several days later, allows for great sensitivity and specificity in the identification of microorganisms while also providing the information on what is dominant within the community. Antibiotic therapy can then be tailored to the chronic infection. Molecular diagnosis also provides a way to assess the efficacy of treatment. Chronic infections are more prevalent and costly than heart disease, cancer, diabetes or any other disease in our healthcare system. Molecular methods for identifying microorganisms provide a powerful diagnostic tool for the management of chronic infections.