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The best strategy for ensuring high quality drinking water is to adopt a multi-barrierapproach which includes maintaining minimal pathogen loading in raw water through sourceprotection, disinfection and filtration at the treatment plant, and maintaining a disinfectantresidual in the distribution system. Increasing the effectiveness of the first barrier decreases theburden on later barriers and provides for greater confidence in water treatment. A key componentof any source water protection (SWP) program is an understanding of the characteristics of thewatershed. This includes information on pathogen baseline concentrations, sources ofcontamination, routes of pathogen transport, and sites of pathogen input. However, typicalmonitoring programs use conventional microscopic or culturing techniques which focus on eitherindividual pathogens or indicators. A more informative pathogen monitoring program (PMP)would provide occurrence data on a broad array of potential pathogens, indicate whether there ishuman or animal source of contamination, and differentiate between wildlife or livestockgenerated animal contamination. Molecular-based techniques such as the polymerase chainreaction (PCR) can be used to provide much of this additional information. This paper discusses PCR-basedgenotyping of waterborne protozoa and the application of these methods. Includes 23 references, table.